Starting phenix.real_space_refine
on Sat Sep 28 21:14:15 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqd_23943/09_2024/7mqd_23943.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqd_23943/09_2024/7mqd_23943.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqd_23943/09_2024/7mqd_23943.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqd_23943/09_2024/7mqd_23943.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqd_23943/09_2024/7mqd_23943.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqd_23943/09_2024/7mqd_23943.cif"
  }
  resolution = 3.25
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 10912 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     P      16      5.49       5
     S      48      5.16       5
     C    7632      2.51       5
     N    2176      2.21       5
     O    2088      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 48 residue(s): 0.24s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 11960
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1449
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 199, 1449
          Classifications: {'peptide': 199}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 40}
          Link IDs: {'PTRANS': 5, 'TRANS': 193}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 135
          Unresolved non-hydrogen angles: 167
          Unresolved non-hydrogen dihedrals: 103
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 4, 'ASP:plan': 11}
          Unresolved non-hydrogen planarities: 101
    Chain: "B"
      Number of atoms: 46
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 46
          Classifications: {'RNA': 2}
          Modifications used: {'rna3p_pur': 2}
          Link IDs: {'rna3p': 1}
  Restraints were copied for chains:
    C, E, G, I, K, M, O, D, F, H, J, L, N, P
  Time building chain proxies: 4.09, per 1000 atoms: 0.34
  Number of scatterers: 11960
  At special positions: 0
  Unit cell: (105.4, 105.4, 85.56, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      48     16.00
     P      16     15.00
     O    2088      8.00
     N    2176      7.00
     C    7632      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: 2.90
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3024

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 8 sheets defined
      46.7% alpha, 13.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 62 through 71
    Processing helix  chain 'A' and resid 80 through 93
      removed outlier: 3.911A  pdb=" N   ASP A  84 " --> pdb=" O   PHE A  80 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ALA A  86 " --> pdb=" O   ARG A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 110
    Processing helix  chain 'A' and resid 117 through 127
    Processing helix  chain 'A' and resid 145 through 155
      removed outlier: 3.501A  pdb=" N   ASP A 155 " --> pdb=" O   TYR A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 173
    Processing helix  chain 'A' and resid 175 through 196
      Proline residue:  A 187  - end of helix
    Processing helix  chain 'C' and resid 62 through 71
    Processing helix  chain 'C' and resid 80 through 93
      removed outlier: 3.912A  pdb=" N   ASP C  84 " --> pdb=" O   PHE C  80 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ALA C  86 " --> pdb=" O   ARG C  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 102 through 110
    Processing helix  chain 'C' and resid 117 through 127
    Processing helix  chain 'C' and resid 145 through 155
    Processing helix  chain 'C' and resid 158 through 173
    Processing helix  chain 'C' and resid 175 through 196
      Proline residue:  C 187  - end of helix
    Processing helix  chain 'E' and resid 62 through 71
    Processing helix  chain 'E' and resid 80 through 93
      removed outlier: 3.911A  pdb=" N   ASP E  84 " --> pdb=" O   PHE E  80 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ALA E  86 " --> pdb=" O   ARG E  82 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 102 through 110
    Processing helix  chain 'E' and resid 117 through 127
    Processing helix  chain 'E' and resid 145 through 155
      removed outlier: 3.501A  pdb=" N   ASP E 155 " --> pdb=" O   TYR E 151 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 158 through 173
    Processing helix  chain 'E' and resid 175 through 196
      Proline residue:  E 187  - end of helix
    Processing helix  chain 'G' and resid 62 through 71
    Processing helix  chain 'G' and resid 80 through 93
      removed outlier: 3.912A  pdb=" N   ASP G  84 " --> pdb=" O   PHE G  80 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ALA G  86 " --> pdb=" O   ARG G  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 102 through 110
    Processing helix  chain 'G' and resid 117 through 127
    Processing helix  chain 'G' and resid 145 through 155
      removed outlier: 3.501A  pdb=" N   ASP G 155 " --> pdb=" O   TYR G 151 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 158 through 173
    Processing helix  chain 'G' and resid 175 through 196
      Proline residue:  G 187  - end of helix
    Processing helix  chain 'I' and resid 62 through 71
    Processing helix  chain 'I' and resid 80 through 93
      removed outlier: 3.911A  pdb=" N   ASP I  84 " --> pdb=" O   PHE I  80 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ALA I  86 " --> pdb=" O   ARG I  82 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 102 through 110
    Processing helix  chain 'I' and resid 117 through 127
    Processing helix  chain 'I' and resid 145 through 155
      removed outlier: 3.501A  pdb=" N   ASP I 155 " --> pdb=" O   TYR I 151 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 158 through 173
    Processing helix  chain 'I' and resid 175 through 196
      Proline residue:  I 187  - end of helix
    Processing helix  chain 'K' and resid 62 through 71
    Processing helix  chain 'K' and resid 80 through 93
      removed outlier: 3.912A  pdb=" N   ASP K  84 " --> pdb=" O   PHE K  80 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ALA K  86 " --> pdb=" O   ARG K  82 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 102 through 110
    Processing helix  chain 'K' and resid 117 through 127
    Processing helix  chain 'K' and resid 145 through 155
      removed outlier: 3.501A  pdb=" N   ASP K 155 " --> pdb=" O   TYR K 151 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 158 through 173
    Processing helix  chain 'K' and resid 175 through 196
      Proline residue:  K 187  - end of helix
    Processing helix  chain 'M' and resid 62 through 71
    Processing helix  chain 'M' and resid 80 through 93
      removed outlier: 3.912A  pdb=" N   ASP M  84 " --> pdb=" O   PHE M  80 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ALA M  86 " --> pdb=" O   ARG M  82 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 102 through 110
    Processing helix  chain 'M' and resid 117 through 127
    Processing helix  chain 'M' and resid 145 through 155
      removed outlier: 3.501A  pdb=" N   ASP M 155 " --> pdb=" O   TYR M 151 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 158 through 173
    Processing helix  chain 'M' and resid 175 through 196
      Proline residue:  M 187  - end of helix
    Processing helix  chain 'O' and resid 62 through 71
    Processing helix  chain 'O' and resid 80 through 93
      removed outlier: 3.911A  pdb=" N   ASP O  84 " --> pdb=" O   PHE O  80 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ALA O  86 " --> pdb=" O   ARG O  82 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 102 through 110
    Processing helix  chain 'O' and resid 117 through 127
    Processing helix  chain 'O' and resid 145 through 155
      removed outlier: 3.501A  pdb=" N   ASP O 155 " --> pdb=" O   TYR O 151 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 158 through 173
    Processing helix  chain 'O' and resid 175 through 196
      Proline residue:  O 187  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8
      removed outlier: 6.181A  pdb=" N   ARG A   5 " --> pdb=" O   VAL A  52 " (cutoff:3.500A)
      removed outlier: 7.337A  pdb=" N   GLN A  54 " --> pdb=" O   ARG A   5 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   HIS A   7 " --> pdb=" O   GLN A  54 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   GLU A  27 " --> pdb=" O   CYS A  39 " (cutoff:3.500A)
      removed outlier: 4.836A  pdb=" N   VAL A  41 " --> pdb=" O   ASP A  25 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   ASP A  25 " --> pdb=" O   VAL A  41 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   LEU A  43 " --> pdb=" O   ALA A  23 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   ALA A  23 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 4 through 8
      removed outlier: 6.181A  pdb=" N   ARG C   5 " --> pdb=" O   VAL C  52 " (cutoff:3.500A)
      removed outlier: 7.337A  pdb=" N   GLN C  54 " --> pdb=" O   ARG C   5 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   HIS C   7 " --> pdb=" O   GLN C  54 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   GLU C  27 " --> pdb=" O   CYS C  39 " (cutoff:3.500A)
      removed outlier: 4.836A  pdb=" N   VAL C  41 " --> pdb=" O   ASP C  25 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   ASP C  25 " --> pdb=" O   VAL C  41 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   LEU C  43 " --> pdb=" O   ALA C  23 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   ALA C  23 " --> pdb=" O   LEU C  43 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 4 through 8
      removed outlier: 6.180A  pdb=" N   ARG E   5 " --> pdb=" O   VAL E  52 " (cutoff:3.500A)
      removed outlier: 7.337A  pdb=" N   GLN E  54 " --> pdb=" O   ARG E   5 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   HIS E   7 " --> pdb=" O   GLN E  54 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   GLU E  27 " --> pdb=" O   CYS E  39 " (cutoff:3.500A)
      removed outlier: 4.836A  pdb=" N   VAL E  41 " --> pdb=" O   ASP E  25 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   ASP E  25 " --> pdb=" O   VAL E  41 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   LEU E  43 " --> pdb=" O   ALA E  23 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   ALA E  23 " --> pdb=" O   LEU E  43 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'G' and resid 4 through 8
      removed outlier: 6.180A  pdb=" N   ARG G   5 " --> pdb=" O   VAL G  52 " (cutoff:3.500A)
      removed outlier: 7.337A  pdb=" N   GLN G  54 " --> pdb=" O   ARG G   5 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   HIS G   7 " --> pdb=" O   GLN G  54 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   GLU G  27 " --> pdb=" O   CYS G  39 " (cutoff:3.500A)
      removed outlier: 4.836A  pdb=" N   VAL G  41 " --> pdb=" O   ASP G  25 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   ASP G  25 " --> pdb=" O   VAL G  41 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   LEU G  43 " --> pdb=" O   ALA G  23 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   ALA G  23 " --> pdb=" O   LEU G  43 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'I' and resid 4 through 8
      removed outlier: 6.181A  pdb=" N   ARG I   5 " --> pdb=" O   VAL I  52 " (cutoff:3.500A)
      removed outlier: 7.336A  pdb=" N   GLN I  54 " --> pdb=" O   ARG I   5 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   HIS I   7 " --> pdb=" O   GLN I  54 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   GLU I  27 " --> pdb=" O   CYS I  39 " (cutoff:3.500A)
      removed outlier: 4.835A  pdb=" N   VAL I  41 " --> pdb=" O   ASP I  25 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   ASP I  25 " --> pdb=" O   VAL I  41 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   LEU I  43 " --> pdb=" O   ALA I  23 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   ALA I  23 " --> pdb=" O   LEU I  43 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'K' and resid 4 through 8
      removed outlier: 6.181A  pdb=" N   ARG K   5 " --> pdb=" O   VAL K  52 " (cutoff:3.500A)
      removed outlier: 7.337A  pdb=" N   GLN K  54 " --> pdb=" O   ARG K   5 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   HIS K   7 " --> pdb=" O   GLN K  54 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   GLU K  27 " --> pdb=" O   CYS K  39 " (cutoff:3.500A)
      removed outlier: 4.836A  pdb=" N   VAL K  41 " --> pdb=" O   ASP K  25 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   ASP K  25 " --> pdb=" O   VAL K  41 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   LEU K  43 " --> pdb=" O   ALA K  23 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   ALA K  23 " --> pdb=" O   LEU K  43 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'M' and resid 4 through 8
      removed outlier: 6.181A  pdb=" N   ARG M   5 " --> pdb=" O   VAL M  52 " (cutoff:3.500A)
      removed outlier: 7.336A  pdb=" N   GLN M  54 " --> pdb=" O   ARG M   5 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   HIS M   7 " --> pdb=" O   GLN M  54 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   GLU M  27 " --> pdb=" O   CYS M  39 " (cutoff:3.500A)
      removed outlier: 4.836A  pdb=" N   VAL M  41 " --> pdb=" O   ASP M  25 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   ASP M  25 " --> pdb=" O   VAL M  41 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   LEU M  43 " --> pdb=" O   ALA M  23 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   ALA M  23 " --> pdb=" O   LEU M  43 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'O' and resid 4 through 8
      removed outlier: 6.181A  pdb=" N   ARG O   5 " --> pdb=" O   VAL O  52 " (cutoff:3.500A)
      removed outlier: 7.337A  pdb=" N   GLN O  54 " --> pdb=" O   ARG O   5 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   HIS O   7 " --> pdb=" O   GLN O  54 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   GLU O  27 " --> pdb=" O   CYS O  39 " (cutoff:3.500A)
      removed outlier: 4.836A  pdb=" N   VAL O  41 " --> pdb=" O   ASP O  25 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   ASP O  25 " --> pdb=" O   VAL O  41 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   LEU O  43 " --> pdb=" O   ALA O  23 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   ALA O  23 " --> pdb=" O   LEU O  43 " (cutoff:3.500A)

    553 hydrogen bonds defined for protein.
    1659 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.99

  Time building geometry restraints manager: 3.38 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: 3841
        1.34 -     1.45: 1632
        1.45 -     1.57: 6655
        1.57 -     1.69: 24
        1.69 -     1.81: 64
  Bond restraints: 12216
  Sorted by residual:
  bond pdb=" N   VAL A 156 "
       pdb=" CA  VAL A 156 "
    ideal  model  delta    sigma   weight residual
    1.456  1.463 -0.007 1.08e-02 8.57e+03 4.43e-01
  bond pdb=" N   VAL M 156 "
       pdb=" CA  VAL M 156 "
    ideal  model  delta    sigma   weight residual
    1.456  1.463 -0.007 1.08e-02 8.57e+03 4.28e-01
  bond pdb=" CB  VAL I  40 "
       pdb=" CG1 VAL I  40 "
    ideal  model  delta    sigma   weight residual
    1.521  1.500  0.021 3.30e-02 9.18e+02 4.13e-01
  bond pdb=" CB  VAL C  40 "
       pdb=" CG1 VAL C  40 "
    ideal  model  delta    sigma   weight residual
    1.521  1.500  0.021 3.30e-02 9.18e+02 4.02e-01
  bond pdb=" C   ARG M 161 "
       pdb=" O   ARG M 161 "
    ideal  model  delta    sigma   weight residual
    1.237  1.244 -0.007 1.17e-02 7.31e+03 3.94e-01
  ... (remaining 12211 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.13: 15748
        1.13 -     2.26: 771
        2.26 -     3.40: 140
        3.40 -     4.53: 21
        4.53 -     5.66: 32
  Bond angle restraints: 16712
  Sorted by residual:
  angle pdb=" CA  GLN A  42 "
        pdb=" CB  GLN A  42 "
        pdb=" CG  GLN A  42 "
      ideal   model   delta    sigma   weight residual
     114.10  119.76   -5.66 2.00e+00 2.50e-01 8.01e+00
  angle pdb=" CA  GLN C  42 "
        pdb=" CB  GLN C  42 "
        pdb=" CG  GLN C  42 "
      ideal   model   delta    sigma   weight residual
     114.10  119.75   -5.65 2.00e+00 2.50e-01 7.99e+00
  angle pdb=" CA  GLN M  42 "
        pdb=" CB  GLN M  42 "
        pdb=" CG  GLN M  42 "
      ideal   model   delta    sigma   weight residual
     114.10  119.73   -5.63 2.00e+00 2.50e-01 7.92e+00
  angle pdb=" CA  GLN I  42 "
        pdb=" CB  GLN I  42 "
        pdb=" CG  GLN I  42 "
      ideal   model   delta    sigma   weight residual
     114.10  119.72   -5.62 2.00e+00 2.50e-01 7.89e+00
  angle pdb=" CA  GLN O  42 "
        pdb=" CB  GLN O  42 "
        pdb=" CG  GLN O  42 "
      ideal   model   delta    sigma   weight residual
     114.10  119.71   -5.61 2.00e+00 2.50e-01 7.88e+00
  ... (remaining 16707 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 6754
       17.83 -    35.66: 318
       35.66 -    53.49: 80
       53.49 -    71.32: 64
       71.32 -    89.15: 16
  Dihedral angle restraints: 7232
    sinusoidal: 2600
      harmonic: 4632
  Sorted by residual:
  dihedral pdb=" CA  PHE A  78 "
           pdb=" C   PHE A  78 "
           pdb=" N   HIS A  79 "
           pdb=" CA  HIS A  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.64   22.36     0      5.00e+00 4.00e-02 2.00e+01
  dihedral pdb=" CA  PHE C  78 "
           pdb=" C   PHE C  78 "
           pdb=" N   HIS C  79 "
           pdb=" CA  HIS C  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.66   22.34     0      5.00e+00 4.00e-02 2.00e+01
  dihedral pdb=" CA  PHE G  78 "
           pdb=" C   PHE G  78 "
           pdb=" N   HIS G  79 "
           pdb=" CA  HIS G  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.68   22.32     0      5.00e+00 4.00e-02 1.99e+01
  ... (remaining 7229 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1071
       0.028 -    0.056: 526
       0.056 -    0.083: 256
       0.083 -    0.111: 131
       0.111 -    0.139: 64
  Chirality restraints: 2048
  Sorted by residual:
  chirality pdb=" CA  ILE G   4 "
            pdb=" N   ILE G   4 "
            pdb=" C   ILE G   4 "
            pdb=" CB  ILE G   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.83e-01
  chirality pdb=" CA  ILE M   4 "
            pdb=" N   ILE M   4 "
            pdb=" C   ILE M   4 "
            pdb=" CB  ILE M   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.79e-01
  chirality pdb=" CA  ILE I   4 "
            pdb=" N   ILE I   4 "
            pdb=" C   ILE I   4 "
            pdb=" CB  ILE I   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.76e-01
  ... (remaining 2045 not shown)

  Planarity restraints: 2048
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE G  83 "   -0.007 2.00e-02 2.50e+03   1.32e-02 1.76e+00
        pdb=" C   PHE G  83 "    0.023 2.00e-02 2.50e+03
        pdb=" O   PHE G  83 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ASP G  84 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE E  83 "   -0.007 2.00e-02 2.50e+03   1.32e-02 1.73e+00
        pdb=" C   PHE E  83 "    0.023 2.00e-02 2.50e+03
        pdb=" O   PHE E  83 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ASP E  84 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE O  83 "   -0.007 2.00e-02 2.50e+03   1.31e-02 1.72e+00
        pdb=" C   PHE O  83 "    0.023 2.00e-02 2.50e+03
        pdb=" O   PHE O  83 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ASP O  84 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 2045 not shown)

  Histogram of nonbonded interaction distances:
        2.46 -     2.94: 5116
        2.94 -     3.43: 11286
        3.43 -     3.92: 19745
        3.92 -     4.41: 23107
        4.41 -     4.90: 37981
  Nonbonded interactions: 97235
  Sorted by model distance:
  nonbonded pdb=" O   HIS G 205 "
            pdb=" NZ  LYS O 103 "
     model   vdw
     2.456 3.120
  nonbonded pdb=" NZ  LYS E 103 "
            pdb=" O   HIS I 205 "
     model   vdw
     2.490 3.120
  nonbonded pdb=" OG1 THR G  26 "
            pdb=" OD1 ASP G  84 "
     model   vdw
     2.499 3.040
  nonbonded pdb=" OG1 THR C  26 "
            pdb=" OD1 ASP C  84 "
     model   vdw
     2.499 3.040
  nonbonded pdb=" OG1 THR I  26 "
            pdb=" OD1 ASP I  84 "
     model   vdw
     2.499 3.040
  ... (remaining 97230 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.160
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.130
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     24.590
  Find NCS groups from input model:        0.380
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
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      :  0.003   0.021  12216  Z= 0.209
  Angle     :  0.617   5.660  16712  Z= 0.372
  Chirality :  0.046   0.139   2048
  Planarity :  0.004   0.026   2048
  Dihedral  : 14.589  89.151   4208
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 1.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.21), residues: 1560
  helix:  0.79 (0.19), residues: 704
  sheet:  0.50 (0.22), residues: 240
  loop :  0.94 (0.28), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP M 197 
 HIS   0.002   0.001   HIS E 116 
 PHE   0.013   0.002   PHE K  78 
 TYR   0.005   0.001   TYR M  17 
 ARG   0.009   0.002   ARG C  37 

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1376 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 1.389 
Fit side-chains
REVERT: A  137 SER cc_start: 0.8402 (t) cc_final: 0.8122 (p)
REVERT: A  146 ARG cc_start: 0.7689 (tpt170) cc_final: 0.7413 (tpp-160)
REVERT: C  146 ARG cc_start: 0.7610 (tpt170) cc_final: 0.7176 (tpp-160)
REVERT: E  146 ARG cc_start: 0.7698 (tpt170) cc_final: 0.7277 (tpp-160)
REVERT: G  146 ARG cc_start: 0.7808 (tpt170) cc_final: 0.7471 (tpp-160)
REVERT: I  146 ARG cc_start: 0.7775 (tpt170) cc_final: 0.7423 (tpp-160)
REVERT: K  137 SER cc_start: 0.8430 (t) cc_final: 0.8148 (p)
REVERT: M  146 ARG cc_start: 0.7579 (tpt170) cc_final: 0.7288 (tpp-160)
REVERT: O  146 ARG cc_start: 0.7612 (tpt170) cc_final: 0.7170 (tpp-160)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.2525
  time to fit residues: 50.8412
Evaluate side-chains
  137 residues out of total 1376 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 1.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 128 optimal weight:    7.9990
   chunk 115 optimal weight:    1.9990
   chunk 63 optimal weight:    4.9990
   chunk 39 optimal weight:    8.9990
   chunk 77 optimal weight:    8.9990
   chunk 61 optimal weight:   10.0000
   chunk 119 optimal weight:    9.9990
   chunk 46 optimal weight:    7.9990
   chunk 72 optimal weight:    6.9990
   chunk 88 optimal weight:    0.9980
   chunk 138 optimal weight:   10.0000
   overall best weight:    4.5988

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

Flipped N/Q/H residues before XYZ refinement:
K 184 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.1715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.041  12216  Z= 0.452
  Angle     :  0.586   4.580  16712  Z= 0.307
  Chirality :  0.048   0.132   2048
  Planarity :  0.004   0.033   2048
  Dihedral  : 11.359  63.774   1968
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  1.52 %
    Favored  : 97.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.52 (0.22), residues: 1560
  helix:  1.47 (0.20), residues: 704
  sheet:  0.63 (0.27), residues: 240
  loop :  0.84 (0.29), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP I 197 
 HIS   0.005   0.001   HIS O 116 
 PHE   0.016   0.002   PHE M  78 
 TYR   0.013   0.002   TYR O  17 
 ARG   0.004   0.001   ARG A 172 

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1376 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 126
  time to evaluate  : 1.442 
Fit side-chains
REVERT: C   25 ASP cc_start: 0.7508 (t0) cc_final: 0.7178 (t0)
REVERT: G   25 ASP cc_start: 0.7520 (t0) cc_final: 0.7143 (t0)
REVERT: K  146 ARG cc_start: 0.7454 (tpp-160) cc_final: 0.7227 (tpp-160)
REVERT: O   25 ASP cc_start: 0.7519 (t0) cc_final: 0.7160 (t0)
  outliers start: 8
  outliers final: 0
  residues processed: 126
  average time/residue: 0.2500
  time to fit residues: 45.7900
Evaluate side-chains
  124 residues out of total 1376 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 1.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 76 optimal weight:   10.0000
   chunk 42 optimal weight:    8.9990
   chunk 114 optimal weight:   10.0000
   chunk 93 optimal weight:    0.7980
   chunk 38 optimal weight:   10.0000
   chunk 138 optimal weight:    5.9990
   chunk 149 optimal weight:    0.9990
   chunk 123 optimal weight:    7.9990
   chunk 137 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 110 optimal weight:    3.9990
   overall best weight:    2.5588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.1959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  12216  Z= 0.268
  Angle     :  0.464   4.462  16712  Z= 0.247
  Chirality :  0.044   0.125   2048
  Planarity :  0.004   0.032   2048
  Dihedral  : 11.224  63.794   1968
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 1.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  2.84 %
    Favored  : 96.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (0.22), residues: 1560
  helix:  1.51 (0.20), residues: 704
  sheet:  1.03 (0.27), residues: 240
  loop :  0.69 (0.28), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E 197 
 HIS   0.003   0.001   HIS M 116 
 PHE   0.013   0.002   PHE E  78 
 TYR   0.009   0.001   TYR K  17 
 ARG   0.001   0.000   ARG C 189 

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1376 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 120
  time to evaluate  : 1.407 
Fit side-chains
REVERT: A  146 ARG cc_start: 0.8005 (tpt-90) cc_final: 0.7553 (tpp-160)
REVERT: C   25 ASP cc_start: 0.7248 (t0) cc_final: 0.6992 (t0)
REVERT: E  146 ARG cc_start: 0.8030 (tpt-90) cc_final: 0.7623 (tpp-160)
REVERT: G   27 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7608 (mm-30)
REVERT: G  146 ARG cc_start: 0.8048 (tpt-90) cc_final: 0.7634 (tpp-160)
REVERT: I  146 ARG cc_start: 0.8017 (tpt-90) cc_final: 0.7546 (tpp-160)
REVERT: O  146 ARG cc_start: 0.8008 (tpt-90) cc_final: 0.7592 (tpp-160)
  outliers start: 8
  outliers final: 0
  residues processed: 120
  average time/residue: 0.2318
  time to fit residues: 41.4069
Evaluate side-chains
  120 residues out of total 1376 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 1.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 136 optimal weight:    3.9990
   chunk 103 optimal weight:    6.9990
   chunk 71 optimal weight:    6.9990
   chunk 15 optimal weight:    4.9990
   chunk 65 optimal weight:    0.8980
   chunk 92 optimal weight:    4.9990
   chunk 138 optimal weight:    7.9990
   chunk 146 optimal weight:    5.9990
   chunk 72 optimal weight:    2.9990
   chunk 131 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   overall best weight:    2.1186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.2071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  12216  Z= 0.227
  Angle     :  0.434   4.454  16712  Z= 0.232
  Chirality :  0.044   0.123   2048
  Planarity :  0.003   0.030   2048
  Dihedral  : 11.136  63.779   1968
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 1.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.22), residues: 1560
  helix:  1.51 (0.20), residues: 704
  sheet:  1.23 (0.27), residues: 240
  loop :  0.63 (0.28), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP I 197 
 HIS   0.002   0.001   HIS O 116 
 PHE   0.011   0.001   PHE C  78 
 TYR   0.008   0.001   TYR A  17 
 ARG   0.001   0.000   ARG G 146 

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1376 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 1.298 
Fit side-chains
REVERT: G   27 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7531 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.1813
  time to fit residues: 32.9951
Evaluate side-chains
  112 residues out of total 1376 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 1.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 122 optimal weight:    7.9990
   chunk 83 optimal weight:    7.9990
   chunk 2 optimal weight:   10.0000
   chunk 109 optimal weight:    9.9990
   chunk 60 optimal weight:    7.9990
   chunk 125 optimal weight:    7.9990
   chunk 101 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 75 optimal weight:    6.9990
   chunk 131 optimal weight:    1.9990
   chunk 37 optimal weight:    5.9990
   overall best weight:    4.7988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.2239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.043  12216  Z= 0.469
  Angle     :  0.548   4.489  16712  Z= 0.285
  Chirality :  0.047   0.132   2048
  Planarity :  0.004   0.036   2048
  Dihedral  : 11.302  63.763   1968
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.21), residues: 1560
  helix:  1.08 (0.20), residues: 704
  sheet:  1.08 (0.27), residues: 240
  loop :  0.36 (0.27), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP K 197 
 HIS   0.004   0.001   HIS O 116 
 PHE   0.010   0.002   PHE C  78 
 TYR   0.015   0.002   TYR E  17 
 ARG   0.002   0.001   ARG E 189 

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1376 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 1.278 
Fit side-chains
REVERT: A  146 ARG cc_start: 0.8055 (tpt170) cc_final: 0.7330 (tpp-160)
REVERT: I  146 ARG cc_start: 0.8059 (tpt170) cc_final: 0.7322 (tpp-160)
REVERT: M  146 ARG cc_start: 0.8044 (tpt170) cc_final: 0.7328 (tpp-160)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.2786
  time to fit residues: 48.0921
Evaluate side-chains
  125 residues out of total 1376 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 1.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 132 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 86 optimal weight:    7.9990
   chunk 36 optimal weight:    0.9980
   chunk 147 optimal weight:    1.9990
   chunk 122 optimal weight:    0.9980
   chunk 68 optimal weight:    8.9990
   chunk 12 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 77 optimal weight:    8.9990
   overall best weight:    1.9986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.2248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  12216  Z= 0.216
  Angle     :  0.422   4.379  16712  Z= 0.227
  Chirality :  0.043   0.123   2048
  Planarity :  0.003   0.032   2048
  Dihedral  : 11.213  63.791   1968
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  2.46 %
    Favored  : 96.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.21), residues: 1560
  helix:  1.36 (0.20), residues: 704
  sheet:  1.28 (0.27), residues: 240
  loop :  0.42 (0.27), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP M 139 
 HIS   0.002   0.001   HIS O 116 
 PHE   0.011   0.001   PHE M  78 
 TYR   0.008   0.001   TYR M  17 
 ARG   0.002   0.000   ARG K  82 

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1376 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 120
  time to evaluate  : 1.282 
Fit side-chains
REVERT: A  146 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7591 (tpp-160)
REVERT: I  146 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7583 (tpp-160)
  outliers start: 10
  outliers final: 1
  residues processed: 130
  average time/residue: 0.2458
  time to fit residues: 46.2267
Evaluate side-chains
  115 residues out of total 1376 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 112
  time to evaluate  : 1.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 ARG
Chi-restraints excluded: chain C residue   42 GLN
Chi-restraints excluded: chain I residue  146 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 141 optimal weight:    7.9990
   chunk 16 optimal weight:    0.5980
   chunk 83 optimal weight:    7.9990
   chunk 107 optimal weight:    8.9990
   chunk 123 optimal weight:    7.9990
   chunk 82 optimal weight:    1.9990
   chunk 146 optimal weight:   10.0000
   chunk 91 optimal weight:    2.9990
   chunk 89 optimal weight:   10.0000
   chunk 67 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9980
   overall best weight:    1.9186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.2339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  12216  Z= 0.210
  Angle     :  0.414   4.383  16712  Z= 0.223
  Chirality :  0.043   0.121   2048
  Planarity :  0.003   0.032   2048
  Dihedral  : 11.164  63.786   1968
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 2.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  2.84 %
    Favored  : 96.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.21), residues: 1560
  helix:  1.41 (0.20), residues: 704
  sheet:  1.47 (0.27), residues: 240
  loop :  0.46 (0.27), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP M 139 
 HIS   0.002   0.000   HIS I 116 
 PHE   0.011   0.001   PHE K  78 
 TYR   0.007   0.001   TYR A  17 
 ARG   0.001   0.000   ARG C 146 

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1376 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 1.318 
Fit side-chains
REVERT: A  146 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7546 (tpp-160)
REVERT: I  146 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7545 (tpp-160)
REVERT: M  146 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7542 (tpp-160)
  outliers start: 11
  outliers final: 1
  residues processed: 124
  average time/residue: 0.2560
  time to fit residues: 45.3057
Evaluate side-chains
  109 residues out of total 1376 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 105
  time to evaluate  : 1.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 ARG
Chi-restraints excluded: chain C residue   42 GLN
Chi-restraints excluded: chain I residue  146 ARG
Chi-restraints excluded: chain M residue  146 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 58 optimal weight:   10.0000
   chunk 87 optimal weight:    6.9990
   chunk 44 optimal weight:    2.9990
   chunk 28 optimal weight:    6.9990
   chunk 93 optimal weight:    3.9990
   chunk 99 optimal weight:    9.9990
   chunk 72 optimal weight:    6.9990
   chunk 13 optimal weight:    9.9990
   chunk 115 optimal weight:   10.0000
   chunk 133 optimal weight:   10.0000
   chunk 140 optimal weight:    6.9990
   overall best weight:    5.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8106
moved from start:          0.2398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.047  12216  Z= 0.544
  Angle     :  0.575   4.589  16712  Z= 0.299
  Chirality :  0.049   0.132   2048
  Planarity :  0.005   0.036   2048
  Dihedral  : 11.322  63.755   1968
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  2.84 %
    Favored  : 96.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.21), residues: 1560
  helix:  0.91 (0.19), residues: 704
  sheet:  0.97 (0.28), residues: 240
  loop :  0.07 (0.26), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP E 197 
 HIS   0.005   0.001   HIS O 116 
 PHE   0.010   0.002   PHE A  78 
 TYR   0.018   0.003   TYR A  17 
 ARG   0.004   0.001   ARG G  82 

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1376 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 1.334 
Fit side-chains
REVERT: M  146 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7072 (tpp-160)
  outliers start: 11
  outliers final: 5
  residues processed: 115
  average time/residue: 0.2318
  time to fit residues: 39.4114
Evaluate side-chains
  113 residues out of total 1376 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 107
  time to evaluate  : 1.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 GLN
Chi-restraints excluded: chain C residue   42 GLN
Chi-restraints excluded: chain E residue   42 GLN
Chi-restraints excluded: chain K residue   42 GLN
Chi-restraints excluded: chain M residue  146 ARG
Chi-restraints excluded: chain O residue   42 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 128 optimal weight:    3.9990
   chunk 136 optimal weight:    0.9980
   chunk 140 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 107 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9990
   chunk 123 optimal weight:    0.9980
   chunk 129 optimal weight:    0.7980
   chunk 89 optimal weight:    0.9980
   chunk 144 optimal weight:    1.9990
   overall best weight:    0.9180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.2405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017  12216  Z= 0.132
  Angle     :  0.385   4.276  16712  Z= 0.213
  Chirality :  0.042   0.122   2048
  Planarity :  0.003   0.031   2048
  Dihedral  : 11.127  63.824   1968
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 1.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.06 %
    Favored  : 99.94 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  :  3.12 %
    Favored  : 96.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.21), residues: 1560
  helix:  1.42 (0.20), residues: 704
  sheet:  1.31 (0.28), residues: 240
  loop :  0.33 (0.27), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP O 139 
 HIS   0.001   0.000   HIS M  79 
 PHE   0.013   0.001   PHE I  78 
 TYR   0.005   0.001   TYR C 151 
 ARG   0.001   0.000   ARG A 146 

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1376 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 105
  time to evaluate  : 1.291 
Fit side-chains
REVERT: M  146 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7560 (tpp-160)
  outliers start: 9
  outliers final: 0
  residues processed: 114
  average time/residue: 0.1855
  time to fit residues: 33.9359
Evaluate side-chains
  106 residues out of total 1376 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 1.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  146 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 88 optimal weight:    6.9990
   chunk 68 optimal weight:    9.9990
   chunk 100 optimal weight:    5.9990
   chunk 151 optimal weight:    5.9990
   chunk 139 optimal weight:    2.9990
   chunk 120 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9990
   chunk 93 optimal weight:    0.9990
   chunk 73 optimal weight:    0.7980
   chunk 95 optimal weight:    5.9990
   chunk 128 optimal weight:   10.0000
   overall best weight:    2.1588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.2377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  12216  Z= 0.233
  Angle     :  0.423   4.403  16712  Z= 0.227
  Chirality :  0.043   0.122   2048
  Planarity :  0.003   0.031   2048
  Dihedral  : 11.161  63.789   1968
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  3.60 %
    Favored  : 96.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.21), residues: 1560
  helix:  1.38 (0.20), residues: 704
  sheet:  1.37 (0.27), residues: 240
  loop :  0.38 (0.27), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP G 139 
 HIS   0.002   0.001   HIS O 116 
 PHE   0.011   0.001   PHE K  78 
 TYR   0.008   0.001   TYR M  17 
 ARG   0.002   0.000   ARG M  82 

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

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

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3120 Ramachandran restraints generated.
    1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1376 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 105
  time to evaluate  : 1.329 
Fit side-chains
REVERT: M  146 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7533 (tpp-160)
  outliers start: 3
  outliers final: 1
  residues processed: 108
  average time/residue: 0.1887
  time to fit residues: 32.6235
Evaluate side-chains
  107 residues out of total 1376 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 105
  time to evaluate  : 1.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   42 GLN
Chi-restraints excluded: chain M residue  146 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 111 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 120 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   chunk 124 optimal weight:    6.9990
   chunk 15 optimal weight:    5.9990
   chunk 22 optimal weight:    5.9990
   chunk 106 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    2.3990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.120345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.100958 restraints weight = 13725.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.3084 rms_B_bonded: 1.46
r_work: 0.2962 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.2808 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.2399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025  12216  Z= 0.254
  Angle     :  0.432   4.444  16712  Z= 0.232
  Chirality :  0.044   0.122   2048
  Planarity :  0.003   0.032   2048
  Dihedral  : 11.172  63.773   1968
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 2.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  3.12 %
    Favored  : 96.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.21), residues: 1560
  helix:  1.37 (0.20), residues: 704
  sheet:  1.38 (0.27), residues: 240
  loop :  0.37 (0.27), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP K 197 
 HIS   0.002   0.001   HIS E 116 
 PHE   0.012   0.001   PHE I  78 
 TYR   0.008   0.001   TYR I  17 
 ARG   0.002   0.000   ARG M  82 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1991.40 seconds
wall clock time: 36 minutes 29.38 seconds (2189.38 seconds total)