Starting phenix.real_space_refine
on Mon Sep 23 15:49:38 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gbr_29920/09_2024/8gbr_29920.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gbr_29920/09_2024/8gbr_29920.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gbr_29920/09_2024/8gbr_29920.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gbr_29920/09_2024/8gbr_29920.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gbr_29920/09_2024/8gbr_29920.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gbr_29920/09_2024/8gbr_29920.cif"
  }
  resolution = 3.4
  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=   0.005
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       5      5.16       5
     C    2345      2.51       5
     N     600      2.21       5
     O     680      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 3630
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 726
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 4, 'TRANS': 88}
          Chain breaks: 1
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 2.01, per 1000 atoms: 0.55
  Number of scatterers: 3630
  At special positions: 0
  Unit cell: (87.978, 70.004, 42.57, 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       5     16.00
     O     680      8.00
     N     600      7.00
     C    2345      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: 0.78
  Conformation dependent library (CDL) restraints added in 421.6 milliseconds
  

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  880

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 10 sheets defined
      0.0% alpha, 51.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.54
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 13 through 16
      removed outlier: 6.395A  pdb=" N   VAL A  14 " --> pdb=" O   LYS C  15 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   VAL C  14 " --> pdb=" O   LYS E  15 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 19 through 20
      removed outlier: 6.600A  pdb=" N   ALA B  19 " --> pdb=" O   VAL D  20 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   ALA A  19 " --> pdb=" O   VAL B  20 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 25 through 34
      removed outlier: 6.593A  pdb=" N   ALA B  25 " --> pdb=" O   ILE D  26 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   VAL D  28 " --> pdb=" O   ALA B  25 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   ASN B  27 " --> pdb=" O   VAL D  28 " (cutoff:3.500A)
      removed outlier: 7.751A  pdb=" N   VAL D  30 " --> pdb=" O   ASN B  27 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   ALA B  29 " --> pdb=" O   VAL D  30 " (cutoff:3.500A)
      removed outlier: 8.110A  pdb=" N   VAL D  32 " --> pdb=" O   ALA B  29 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   HIS B  31 " --> pdb=" O   VAL D  32 " (cutoff:3.500A)
      removed outlier: 8.166A  pdb=" N   ARG D  34 " --> pdb=" O   HIS B  31 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   PHE B  33 " --> pdb=" O   ARG D  34 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   ALA A  25 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
      removed outlier: 7.890A  pdb=" N   VAL B  28 " --> pdb=" O   ALA A  25 " (cutoff:3.500A)
      removed outlier: 6.142A  pdb=" N   ASN A  27 " --> pdb=" O   VAL B  28 " (cutoff:3.500A)
      removed outlier: 7.721A  pdb=" N   VAL B  30 " --> pdb=" O   ASN A  27 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   ALA A  29 " --> pdb=" O   VAL B  30 " (cutoff:3.500A)
      removed outlier: 8.080A  pdb=" N   VAL B  32 " --> pdb=" O   ALA A  29 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   HIS A  31 " --> pdb=" O   VAL B  32 " (cutoff:3.500A)
      removed outlier: 8.135A  pdb=" N   ARG B  34 " --> pdb=" O   HIS A  31 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   PHE A  33 " --> pdb=" O   ARG B  34 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 59 through 66
      removed outlier: 6.847A  pdb=" N   PHE B  64 " --> pdb=" O   GLU D  63 " (cutoff:3.500A)
      removed outlier: 7.034A  pdb=" N   VAL D  65 " --> pdb=" O   PHE B  64 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   GLU B  66 " --> pdb=" O   VAL D  65 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   PHE A  64 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   VAL B  65 " --> pdb=" O   PHE A  64 " (cutoff:3.500A)
      removed outlier: 7.044A  pdb=" N   GLU A  66 " --> pdb=" O   VAL B  65 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   THR A  59 " --> pdb=" O   THR C  60 " (cutoff:3.500A)
      removed outlier: 8.300A  pdb=" N   GLU C  62 " --> pdb=" O   THR A  59 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   GLU A  61 " --> pdb=" O   GLU C  62 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   PHE C  64 " --> pdb=" O   GLU A  61 " (cutoff:3.500A)
      removed outlier: 7.493A  pdb=" N   GLU A  63 " --> pdb=" O   PHE C  64 " (cutoff:3.500A)
      removed outlier: 10.313A  pdb=" N   GLU C  66 " --> pdb=" O   GLU A  63 " (cutoff:3.500A)
      removed outlier: 9.143A  pdb=" N   VAL A  65 " --> pdb=" O   GLU C  66 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   THR C  59 " --> pdb=" O   THR E  60 " (cutoff:3.500A)
      removed outlier: 8.332A  pdb=" N   GLU E  62 " --> pdb=" O   THR C  59 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   GLU C  61 " --> pdb=" O   GLU E  62 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   PHE E  64 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
      removed outlier: 7.533A  pdb=" N   GLU C  63 " --> pdb=" O   PHE E  64 " (cutoff:3.500A)
      removed outlier: 10.345A  pdb=" N   GLU E  66 " --> pdb=" O   GLU C  63 " (cutoff:3.500A)
      removed outlier: 9.179A  pdb=" N   VAL C  65 " --> pdb=" O   GLU E  66 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 69 through 73
      removed outlier: 6.577A  pdb=" N   LYS A  70 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 8.081A  pdb=" N   ILE C  73 " --> pdb=" O   LYS A  70 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   GLU A  72 " --> pdb=" O   ILE C  73 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   LYS C  70 " --> pdb=" O   VAL E  71 " (cutoff:3.500A)
      removed outlier: 8.101A  pdb=" N   ILE E  73 " --> pdb=" O   LYS C  70 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   GLU C  72 " --> pdb=" O   ILE E  73 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 76 through 80
      removed outlier: 7.015A  pdb=" N   SER B  77 " --> pdb=" O   LYS D  76 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   TYR D  78 " --> pdb=" O   SER B  77 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   SER A  77 " --> pdb=" O   LYS B  76 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   TYR B  78 " --> pdb=" O   SER A  77 " (cutoff:3.500A)
      removed outlier: 9.209A  pdb=" N   LYS A  76 " --> pdb=" O   SER C  77 " (cutoff:3.500A)
      removed outlier: 9.832A  pdb=" N   TRP C  79 " --> pdb=" O   LYS A  76 " (cutoff:3.500A)
      removed outlier: 5.702A  pdb=" N   TYR A  78 " --> pdb=" O   TRP C  79 " (cutoff:3.500A)
      removed outlier: 9.246A  pdb=" N   LYS C  76 " --> pdb=" O   SER E  77 " (cutoff:3.500A)
      removed outlier: 9.868A  pdb=" N   TRP E  79 " --> pdb=" O   LYS C  76 " (cutoff:3.500A)
      removed outlier: 5.744A  pdb=" N   TYR C  78 " --> pdb=" O   TRP E  79 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 92 through 99
      removed outlier: 6.810A  pdb=" N   VAL B  93 " --> pdb=" O   VAL D  94 " (cutoff:3.500A)
      removed outlier: 8.127A  pdb=" N   THR D  96 " --> pdb=" O   VAL B  93 " (cutoff:3.500A)
      removed outlier: 6.296A  pdb=" N   PHE B  95 " --> pdb=" O   THR D  96 " (cutoff:3.500A)
      removed outlier: 7.779A  pdb=" N   ASN D  98 " --> pdb=" O   PHE B  95 " (cutoff:3.500A)
      removed outlier: 6.053A  pdb=" N   ALA B  97 " --> pdb=" O   ASN D  98 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   VAL A  93 " --> pdb=" O   VAL B  94 " (cutoff:3.500A)
      removed outlier: 8.139A  pdb=" N   THR B  96 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   PHE A  95 " --> pdb=" O   THR B  96 " (cutoff:3.500A)
      removed outlier: 7.791A  pdb=" N   ASN B  98 " --> pdb=" O   PHE A  95 " (cutoff:3.500A)
      removed outlier: 6.062A  pdb=" N   ALA A  97 " --> pdb=" O   ASN B  98 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 103 through 110
      removed outlier: 6.532A  pdb=" N   ARG B 103 " --> pdb=" O   ARG D 104 " (cutoff:3.500A)
      removed outlier: 8.114A  pdb=" N   THR D 106 " --> pdb=" O   ARG B 103 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   TYR B 105 " --> pdb=" O   THR D 106 " (cutoff:3.500A)
      removed outlier: 8.114A  pdb=" N   ALA D 108 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 9.072A  pdb=" N   ILE B 107 " --> pdb=" O   ALA D 108 " (cutoff:3.500A)
      removed outlier: 7.210A  pdb=" N   LEU D 110 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
      removed outlier: 9.172A  pdb=" N   ALA B 109 " --> pdb=" O   LEU D 110 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   ARG A 103 " --> pdb=" O   ARG B 104 " (cutoff:3.500A)
      removed outlier: 8.120A  pdb=" N   THR B 106 " --> pdb=" O   ARG A 103 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   TYR A 105 " --> pdb=" O   THR B 106 " (cutoff:3.500A)
      removed outlier: 8.117A  pdb=" N   ALA B 108 " --> pdb=" O   TYR A 105 " (cutoff:3.500A)
      removed outlier: 9.062A  pdb=" N   ILE A 107 " --> pdb=" O   ALA B 108 " (cutoff:3.500A)
      removed outlier: 7.194A  pdb=" N   LEU B 110 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
      removed outlier: 9.144A  pdb=" N   ALA A 109 " --> pdb=" O   LEU B 110 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   ALA C 109 " --> pdb=" O   ALA A 108 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   LEU A 110 " --> pdb=" O   ALA C 109 " (cutoff:3.500A)
      removed outlier: 7.070A  pdb=" N   ALA E 109 " --> pdb=" O   ALA C 108 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   LEU C 110 " --> pdb=" O   ALA E 109 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 114 through 115
      removed outlier: 7.054A  pdb=" N   TYR A 114 " --> pdb=" O   SER C 115 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   TYR C 114 " --> pdb=" O   SER E 115 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 118 through 123
      removed outlier: 5.845A  pdb=" N   THR B 118 " --> pdb=" O   THR D 119 " (cutoff:3.500A)
      removed outlier: 7.835A  pdb=" N   VAL D 121 " --> pdb=" O   THR B 118 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   ALA B 120 " --> pdb=" O   VAL D 121 " (cutoff:3.500A)
      removed outlier: 8.275A  pdb=" N   THR D 123 " --> pdb=" O   ALA B 120 " (cutoff:3.500A)
      removed outlier: 7.150A  pdb=" N   VAL B 122 " --> pdb=" O   THR D 123 " (cutoff:3.500A)
      removed outlier: 5.828A  pdb=" N   THR A 118 " --> pdb=" O   THR B 119 " (cutoff:3.500A)
      removed outlier: 7.822A  pdb=" N   VAL B 121 " --> pdb=" O   THR A 118 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   ALA A 120 " --> pdb=" O   VAL B 121 " (cutoff:3.500A)
      removed outlier: 8.267A  pdb=" N   THR B 123 " --> pdb=" O   ALA A 120 " (cutoff:3.500A)
      removed outlier: 7.144A  pdb=" N   VAL A 122 " --> pdb=" O   THR B 123 " (cutoff:3.500A)

    82 hydrogen bonds defined for protein.
    246 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: 0.90

  Time building geometry restraints manager: 0.93 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: 1140
        1.34 -     1.45: 496
        1.45 -     1.57: 2069
        1.57 -     1.68: 0
        1.68 -     1.80: 10
  Bond restraints: 3715
  Sorted by residual:
  bond pdb=" C   MET B  13 "
       pdb=" O   MET B  13 "
    ideal  model  delta    sigma   weight residual
    1.236  1.222  0.013 1.20e-02 6.94e+03 1.24e+00
  bond pdb=" C   MET A  13 "
       pdb=" O   MET A  13 "
    ideal  model  delta    sigma   weight residual
    1.236  1.222  0.013 1.20e-02 6.94e+03 1.23e+00
  bond pdb=" C   MET C  13 "
       pdb=" O   MET C  13 "
    ideal  model  delta    sigma   weight residual
    1.236  1.222  0.013 1.20e-02 6.94e+03 1.23e+00
  bond pdb=" C   MET D  13 "
       pdb=" O   MET D  13 "
    ideal  model  delta    sigma   weight residual
    1.236  1.222  0.013 1.20e-02 6.94e+03 1.22e+00
  bond pdb=" C   MET E  13 "
       pdb=" O   MET E  13 "
    ideal  model  delta    sigma   weight residual
    1.236  1.223  0.012 1.20e-02 6.94e+03 1.06e+00
  ... (remaining 3710 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.76: 4370
        0.76 -     1.52: 545
        1.52 -     2.28: 76
        2.28 -     3.04: 34
        3.04 -     3.80: 30
  Bond angle restraints: 5055
  Sorted by residual:
  angle pdb=" CA  TYR C 114 "
        pdb=" CB  TYR C 114 "
        pdb=" CG  TYR C 114 "
      ideal   model   delta    sigma   weight residual
     113.90  117.20   -3.30 1.80e+00 3.09e-01 3.36e+00
  angle pdb=" CA  TYR A 114 "
        pdb=" CB  TYR A 114 "
        pdb=" CG  TYR A 114 "
      ideal   model   delta    sigma   weight residual
     113.90  117.17   -3.27 1.80e+00 3.09e-01 3.31e+00
  angle pdb=" CA  TYR D 114 "
        pdb=" CB  TYR D 114 "
        pdb=" CG  TYR D 114 "
      ideal   model   delta    sigma   weight residual
     113.90  117.17   -3.27 1.80e+00 3.09e-01 3.30e+00
  angle pdb=" CA  TYR B 114 "
        pdb=" CB  TYR B 114 "
        pdb=" CG  TYR B 114 "
      ideal   model   delta    sigma   weight residual
     113.90  117.15   -3.25 1.80e+00 3.09e-01 3.27e+00
  angle pdb=" CA  TYR E 114 "
        pdb=" CB  TYR E 114 "
        pdb=" CG  TYR E 114 "
      ideal   model   delta    sigma   weight residual
     113.90  117.13   -3.23 1.80e+00 3.09e-01 3.23e+00
  ... (remaining 5050 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.69: 1955
       15.69 -    31.37: 185
       31.37 -    47.06: 35
       47.06 -    62.75: 5
       62.75 -    78.43: 10
  Dihedral angle restraints: 2190
    sinusoidal: 830
      harmonic: 1360
  Sorted by residual:
  dihedral pdb=" CG  ARG B  34 "
           pdb=" CD  ARG B  34 "
           pdb=" NE  ARG B  34 "
           pdb=" CZ  ARG B  34 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   41.41   48.59     2      1.50e+01 4.44e-03 1.20e+01
  dihedral pdb=" CG  ARG C  34 "
           pdb=" CD  ARG C  34 "
           pdb=" NE  ARG C  34 "
           pdb=" CZ  ARG C  34 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   41.46   48.54     2      1.50e+01 4.44e-03 1.20e+01
  dihedral pdb=" CG  ARG A  34 "
           pdb=" CD  ARG A  34 "
           pdb=" NE  ARG A  34 "
           pdb=" CZ  ARG A  34 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   41.47   48.53     2      1.50e+01 4.44e-03 1.20e+01
  ... (remaining 2187 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 260
       0.026 -    0.052: 193
       0.052 -    0.078: 53
       0.078 -    0.104: 42
       0.104 -    0.129: 47
  Chirality restraints: 595
  Sorted by residual:
  chirality pdb=" CA  VAL B  65 "
            pdb=" N   VAL B  65 "
            pdb=" C   VAL B  65 "
            pdb=" CB  VAL B  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.19e-01
  chirality pdb=" CA  VAL E 121 "
            pdb=" N   VAL E 121 "
            pdb=" C   VAL E 121 "
            pdb=" CB  VAL E 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.13e-01
  chirality pdb=" CA  VAL A  65 "
            pdb=" N   VAL A  65 "
            pdb=" C   VAL A  65 "
            pdb=" CB  VAL A  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.11e-01
  ... (remaining 592 not shown)

  Planarity restraints: 625
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER D  23 "    0.035 5.00e-02 4.00e+02   5.32e-02 4.52e+00
        pdb=" N   PRO D  24 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO D  24 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO D  24 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C  23 "    0.035 5.00e-02 4.00e+02   5.31e-02 4.51e+00
        pdb=" N   PRO C  24 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO C  24 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO C  24 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A  23 "    0.035 5.00e-02 4.00e+02   5.31e-02 4.51e+00
        pdb=" N   PRO A  24 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO A  24 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A  24 "    0.029 5.00e-02 4.00e+02
  ... (remaining 622 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 30
        2.68 -     3.23: 3036
        3.23 -     3.79: 5151
        3.79 -     4.34: 7288
        4.34 -     4.90: 12102
  Nonbonded interactions: 27607
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 112 "
            pdb=" O   SER B 112 "
     model   vdw
     2.120 3.040
  nonbonded pdb=" O   SER A 112 "
            pdb=" OG  SER C 112 "
     model   vdw
     2.128 3.040
  nonbonded pdb=" OG  SER B 112 "
            pdb=" O   SER D 112 "
     model   vdw
     2.148 3.040
  nonbonded pdb=" O   SER C 112 "
            pdb=" OG  SER E 112 "
     model   vdw
     2.165 3.040
  nonbonded pdb=" OG1 THR A 119 "
            pdb=" OH  TYR B 114 "
     model   vdw
     2.585 3.040
  ... (remaining 27602 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 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

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:             0.680
  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:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.160
  Find NCS groups from input model:        0.110
  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:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3715  Z= 0.270
  Angle     :  0.593   3.796   5055  Z= 0.343
  Chirality :  0.050   0.129    595
  Planarity :  0.007   0.053    625
  Dihedral  : 13.841  78.434   1310
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.33 %
    Favored  : 93.67 %
  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: -2.35 (0.38), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.79 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E  79 
 HIS   0.001   0.000   HIS D  31 
 PHE   0.008   0.002   PHE B  87 
 TYR   0.016   0.002   TYR E 114 
 ARG   0.009   0.002   ARG B  34 

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 395 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.450 
Fit side-chains
REVERT: A   70 LYS cc_start: 0.8728 (tttt) cc_final: 0.8487 (tttt)
REVERT: A   85 SER cc_start: 0.9353 (m) cc_final: 0.9115 (t)
REVERT: D   70 LYS cc_start: 0.8905 (tttt) cc_final: 0.8376 (tppt)
REVERT: E   34 ARG cc_start: 0.8448 (ttt90) cc_final: 0.7335 (pmt-80)
REVERT: E   76 LYS cc_start: 0.8802 (mttp) cc_final: 0.8438 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 0.1810
  time to fit residues: 34.2602
Evaluate side-chains
  120 residues out of total 395 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 37 optimal weight:    9.9990
   chunk 34 optimal weight:    0.0470
   chunk 18 optimal weight:    0.0030
   chunk 11 optimal weight:    7.9990
   chunk 23 optimal weight:    5.9990
   chunk 35 optimal weight:   10.0000
   chunk 13 optimal weight:    9.9990
   chunk 21 optimal weight:    9.9990
   chunk 26 optimal weight:    7.9990
   chunk 40 optimal weight:    9.9990
   chunk 22 optimal weight:    9.9990
   overall best weight:    4.4094

-------------------------------------------------------------------------------
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: 0.8307
moved from start:          0.3384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   3715  Z= 0.337
  Angle     :  0.654   5.757   5055  Z= 0.340
  Chirality :  0.049   0.136    595
  Planarity :  0.005   0.040    625
  Dihedral  :  4.777  13.317    500
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 16.71 %
    Favored  : 81.01 %
  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: -2.37 (0.37), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.80 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  79 
 HIS   0.001   0.000   HIS E  90 
 PHE   0.019   0.002   PHE D  33 
 TYR   0.014   0.002   TYR C  69 
 ARG   0.007   0.001   ARG D  34 

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 395 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 131
  time to evaluate  : 0.427 
Fit side-chains
REVERT: A   85 SER cc_start: 0.9370 (m) cc_final: 0.9102 (t)
REVERT: D   70 LYS cc_start: 0.8735 (tttt) cc_final: 0.8450 (tppt)
REVERT: E   34 ARG cc_start: 0.8546 (ttt90) cc_final: 0.7648 (pmt-80)
REVERT: E   76 LYS cc_start: 0.8910 (mttp) cc_final: 0.8158 (mmmt)
  outliers start: 9
  outliers final: 8
  residues processed: 134
  average time/residue: 0.1632
  time to fit residues: 26.3028
Evaluate side-chains
  132 residues out of total 395 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 124
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain C residue   62 GLU
Chi-restraints excluded: chain C residue   84 ILE
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   84 ILE
Chi-restraints excluded: chain E residue  111 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 12 optimal weight:    9.9990
   chunk 34 optimal weight:    2.9990
   chunk 27 optimal weight:    9.9990
   chunk 11 optimal weight:   20.0000
   chunk 40 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9990
   chunk 36 optimal weight:   10.0000
   chunk 13 optimal weight:    9.9990
   chunk 32 optimal weight:   10.0000
   chunk 30 optimal weight:    6.9990
   chunk 21 optimal weight:    9.9990
   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: 0.8336
moved from start:          0.4004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   3715  Z= 0.410
  Angle     :  0.648   5.179   5055  Z= 0.344
  Chirality :  0.048   0.133    595
  Planarity :  0.004   0.026    625
  Dihedral  :  4.733  15.635    500
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 15.95 %
    Favored  : 79.75 %
  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: -2.53 (0.36), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.92 (0.27), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D  79 
 HIS   0.003   0.001   HIS C  90 
 PHE   0.014   0.002   PHE D  33 
 TYR   0.009   0.002   TYR A  69 
 ARG   0.006   0.001   ARG D  34 

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 395 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 125
  time to evaluate  : 0.387 
Fit side-chains
REVERT: E   34 ARG cc_start: 0.8515 (ttt90) cc_final: 0.7484 (pmt-80)
REVERT: E   66 GLU cc_start: 0.5985 (pm20) cc_final: 0.5688 (pm20)
REVERT: E   76 LYS cc_start: 0.8789 (mttp) cc_final: 0.8440 (mmmt)
  outliers start: 17
  outliers final: 15
  residues processed: 128
  average time/residue: 0.1564
  time to fit residues: 24.1257
Evaluate side-chains
  133 residues out of total 395 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain C residue   62 GLU
Chi-restraints excluded: chain C residue   84 ILE
Chi-restraints excluded: chain D residue   68 ILE
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue   82 LEU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   68 ILE
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   84 ILE
Chi-restraints excluded: chain E residue  111 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 4 optimal weight:    6.9990
   chunk 19 optimal weight:    7.9990
   chunk 27 optimal weight:    8.9990
   chunk 41 optimal weight:    0.4980
   chunk 43 optimal weight:    0.8980
   chunk 21 optimal weight:    9.9990
   chunk 38 optimal weight:    0.6980
   chunk 11 optimal weight:   20.0000
   chunk 36 optimal weight:   10.0000
   chunk 24 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   overall best weight:    3.4184

-------------------------------------------------------------------------------
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: 0.8307
moved from start:          0.4235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3715  Z= 0.268
  Angle     :  0.618   5.944   5055  Z= 0.321
  Chirality :  0.048   0.131    595
  Planarity :  0.003   0.024    625
  Dihedral  :  4.572  16.241    500
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 15.19 %
    Favored  : 80.51 %
  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: -2.54 (0.37), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.93 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP D  79 
 HIS   0.002   0.001   HIS A  31 
 PHE   0.013   0.002   PHE D  33 
 TYR   0.015   0.001   TYR C  69 
 ARG   0.004   0.001   ARG A  34 

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 395 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 125
  time to evaluate  : 0.478 
Fit side-chains
REVERT: E   34 ARG cc_start: 0.8386 (ttt90) cc_final: 0.7463 (pmt-80)
REVERT: E   76 LYS cc_start: 0.8835 (mttp) cc_final: 0.8465 (mmmt)
  outliers start: 17
  outliers final: 13
  residues processed: 128
  average time/residue: 0.1539
  time to fit residues: 24.3442
Evaluate side-chains
  130 residues out of total 395 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 117
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   76 LYS
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain C residue   84 ILE
Chi-restraints excluded: chain D residue   68 ILE
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   84 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 32 optimal weight:    8.9990
   chunk 17 optimal weight:    5.9990
   chunk 37 optimal weight:    8.9990
   chunk 30 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 22 optimal weight:   20.0000
   chunk 39 optimal weight:    7.9990
   chunk 10 optimal weight:    9.9990
   chunk 14 optimal weight:   10.0000
   chunk 8 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    5.3990

-------------------------------------------------------------------------------
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: 0.8332
moved from start:          0.4551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   3715  Z= 0.392
  Angle     :  0.664   5.644   5055  Z= 0.349
  Chirality :  0.048   0.133    595
  Planarity :  0.003   0.019    625
  Dihedral  :  4.732  15.690    500
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.97 %
    Favored  : 93.03 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 14.43 %
    Favored  : 80.76 %
  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: -2.64 (0.37), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.00 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  79 
 HIS   0.004   0.001   HIS B  90 
 PHE   0.016   0.002   PHE A  33 
 TYR   0.010   0.002   TYR B  78 
 ARG   0.004   0.001   ARG D  34 

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 395 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 119
  time to evaluate  : 0.434 
Fit side-chains
REVERT: E   34 ARG cc_start: 0.8405 (ttt90) cc_final: 0.7512 (pmt-80)
REVERT: E   58 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7275 (mt)
REVERT: E   76 LYS cc_start: 0.8814 (mttp) cc_final: 0.8596 (mmmt)
  outliers start: 19
  outliers final: 15
  residues processed: 125
  average time/residue: 0.1386
  time to fit residues: 21.4316
Evaluate side-chains
  127 residues out of total 395 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain C residue   84 ILE
Chi-restraints excluded: chain D residue   18 ASP
Chi-restraints excluded: chain D residue   68 ILE
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   58 LEU
Chi-restraints excluded: chain E residue   68 ILE
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   84 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 10 optimal weight:   10.0000
   chunk 43 optimal weight:    0.0270
   chunk 36 optimal weight:    9.9990
   chunk 20 optimal weight:   20.0000
   chunk 3 optimal weight:    9.9990
   chunk 14 optimal weight:    9.9990
   chunk 22 optimal weight:   10.0000
   chunk 41 optimal weight:   10.0000
   chunk 4 optimal weight:    4.9990
   chunk 24 optimal weight:    9.9990
   chunk 31 optimal weight:    8.9990
   overall best weight:    6.8046

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

Flipped N/Q/H residues before XYZ refinement:
E  88 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.4705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.044   3715  Z= 0.475
  Angle     :  0.717   6.817   5055  Z= 0.375
  Chirality :  0.048   0.132    595
  Planarity :  0.003   0.018    625
  Dihedral  :  4.850  16.178    500
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 14.18 %
    Favored  : 80.51 %
  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: -2.74 (0.37), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.08 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  79 
 HIS   0.003   0.001   HIS D  88 
 PHE   0.012   0.002   PHE A  95 
 TYR   0.011   0.002   TYR B  78 
 ARG   0.003   0.001   ARG D  34 

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 395 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 110
  time to evaluate  : 0.434 
Fit side-chains
REVERT: C   62 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7035 (tp30)
REVERT: E   34 ARG cc_start: 0.8426 (ttt90) cc_final: 0.7537 (pmt-80)
  outliers start: 21
  outliers final: 18
  residues processed: 116
  average time/residue: 0.1327
  time to fit residues: 19.2943
Evaluate side-chains
  126 residues out of total 395 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain C residue   84 ILE
Chi-restraints excluded: chain D residue   18 ASP
Chi-restraints excluded: chain D residue   68 ILE
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue   84 ILE
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   68 ILE
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   84 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 36 optimal weight:    8.9990
   chunk 43 optimal weight:    0.0470
   chunk 27 optimal weight:    9.9990
   chunk 26 optimal weight:    9.9990
   chunk 20 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 25 optimal weight:    6.9990
   chunk 13 optimal weight:    9.9990
   chunk 8 optimal weight:    7.9990
   chunk 29 optimal weight:    5.9990
   overall best weight:    6.0086

-------------------------------------------------------------------------------
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: 0.8331
moved from start:          0.4904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056   3715  Z= 0.435
  Angle     :  0.721   6.982   5055  Z= 0.375
  Chirality :  0.048   0.131    595
  Planarity :  0.003   0.019    625
  Dihedral  :  4.866  16.022    500
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.19 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 15.95 %
    Favored  : 78.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.77 (0.37), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.10 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  79 
 HIS   0.003   0.001   HIS D  88 
 PHE   0.018   0.002   PHE A  33 
 TYR   0.010   0.002   TYR B  78 
 ARG   0.003   0.001   ARG A  34 

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 395 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 114
  time to evaluate  : 0.432 
Fit side-chains
REVERT: C   62 GLU cc_start: 0.7362 (mm-30) cc_final: 0.6994 (tp30)
REVERT: E   34 ARG cc_start: 0.8388 (ttt90) cc_final: 0.7517 (pmt-80)
REVERT: E   58 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.6840 (mt)
  outliers start: 20
  outliers final: 18
  residues processed: 119
  average time/residue: 0.1321
  time to fit residues: 19.8274
Evaluate side-chains
  130 residues out of total 395 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue   84 ILE
Chi-restraints excluded: chain D residue   18 ASP
Chi-restraints excluded: chain D residue   68 ILE
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue   84 ILE
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   58 LEU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   84 ILE
Chi-restraints excluded: chain E residue  111 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 21 optimal weight:    9.9990
   chunk 4 optimal weight:    6.9990
   chunk 34 optimal weight:    8.9990
   chunk 39 optimal weight:    0.9980
   chunk 41 optimal weight:    7.9990
   chunk 37 optimal weight:   10.0000
   chunk 40 optimal weight:    0.9980
   chunk 24 optimal weight:   10.0000
   chunk 17 optimal weight:    6.9990
   chunk 31 optimal weight:    6.9990
   chunk 12 optimal weight:    5.9990
   overall best weight:    4.3986

-------------------------------------------------------------------------------
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: 0.8312
moved from start:          0.4951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   3715  Z= 0.351
  Angle     :  0.733   7.807   5055  Z= 0.373
  Chirality :  0.048   0.137    595
  Planarity :  0.003   0.020    625
  Dihedral  :  4.824  16.698    500
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.64 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 15.44 %
    Favored  : 79.24 %
  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: -2.74 (0.37), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.08 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP D  79 
 HIS   0.002   0.001   HIS D  88 
 PHE   0.011   0.001   PHE D  33 
 TYR   0.013   0.002   TYR A  69 
 ARG   0.003   0.001   ARG A  34 

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 395 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 118
  time to evaluate  : 0.491 
Fit side-chains
REVERT: C   62 GLU cc_start: 0.7344 (mm-30) cc_final: 0.6953 (tp30)
REVERT: D   70 LYS cc_start: 0.8863 (tttt) cc_final: 0.8546 (tppt)
REVERT: E   34 ARG cc_start: 0.8377 (ttt90) cc_final: 0.7545 (pmt-80)
REVERT: E   58 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.6856 (mt)
  outliers start: 21
  outliers final: 19
  residues processed: 124
  average time/residue: 0.1412
  time to fit residues: 21.8502
Evaluate side-chains
  135 residues out of total 395 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue   84 ILE
Chi-restraints excluded: chain D residue   18 ASP
Chi-restraints excluded: chain D residue   68 ILE
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   58 LEU
Chi-restraints excluded: chain E residue   68 ILE
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   84 ILE
Chi-restraints excluded: chain E residue  111 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 36 optimal weight:   10.0000
   chunk 38 optimal weight:    9.9990
   chunk 40 optimal weight:    6.9990
   chunk 26 optimal weight:    9.9990
   chunk 42 optimal weight:    7.9990
   chunk 20 optimal weight:   20.0000
   chunk 29 optimal weight:    7.9990
   chunk 44 optimal weight:    3.9990
   chunk 41 optimal weight:    5.9990
   chunk 35 optimal weight:   10.0000
   chunk 3 optimal weight:    9.9990
   overall best weight:    6.5990

-------------------------------------------------------------------------------
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: 0.8332
moved from start:          0.5114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.064   3715  Z= 0.480
  Angle     :  0.771   7.366   5055  Z= 0.400
  Chirality :  0.048   0.145    595
  Planarity :  0.003   0.021    625
  Dihedral  :  4.935  17.704    500
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.54 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  5.82 %
    Allowed  : 15.95 %
    Favored  : 78.23 %
  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: -2.81 (0.37), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.14 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  79 
 HIS   0.003   0.001   HIS D  88 
 PHE   0.017   0.002   PHE A  33 
 TYR   0.033   0.002   TYR C  69 
 ARG   0.003   0.001   ARG D  34 

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 395 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 0.374 
Fit side-chains
REVERT: C   62 GLU cc_start: 0.7332 (mm-30) cc_final: 0.6954 (tp30)
REVERT: D   70 LYS cc_start: 0.8865 (tttt) cc_final: 0.8543 (tppt)
REVERT: E   34 ARG cc_start: 0.8394 (ttt90) cc_final: 0.7553 (pmt-80)
REVERT: E   58 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.6843 (mt)
  outliers start: 23
  outliers final: 22
  residues processed: 119
  average time/residue: 0.1384
  time to fit residues: 20.4802
Evaluate side-chains
  135 residues out of total 395 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 112
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain C residue   84 ILE
Chi-restraints excluded: chain D residue   18 ASP
Chi-restraints excluded: chain D residue   58 LEU
Chi-restraints excluded: chain D residue   68 ILE
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue   82 LEU
Chi-restraints excluded: chain D residue   84 ILE
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   58 LEU
Chi-restraints excluded: chain E residue   68 ILE
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   84 ILE
Chi-restraints excluded: chain E residue  111 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 27 optimal weight:    9.9990
   chunk 21 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 38 optimal weight:    9.9990
   chunk 10 optimal weight:    6.9990
   chunk 32 optimal weight:    0.9990
   chunk 5 optimal weight:    9.9990
   chunk 9 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   chunk 14 optimal weight:    5.9990
   chunk 36 optimal weight:   10.0000
   overall best weight:    2.9988

-------------------------------------------------------------------------------
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: 0.8284
moved from start:          0.5148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   3715  Z= 0.287
  Angle     :  0.743   8.360   5055  Z= 0.380
  Chirality :  0.049   0.138    595
  Planarity :  0.003   0.019    625
  Dihedral  :  4.729  16.416    500
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 17.97 %
    Favored  : 77.97 %
  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: -2.76 (0.37), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.09 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B  79 
 HIS   0.003   0.001   HIS A  31 
 PHE   0.014   0.001   PHE B  33 
 TYR   0.024   0.002   TYR C  69 
 ARG   0.003   0.001   ARG A  34 

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 395 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 0.425 
Fit side-chains
REVERT: A   59 THR cc_start: 0.9554 (m) cc_final: 0.9191 (p)
REVERT: C   62 GLU cc_start: 0.7311 (mm-30) cc_final: 0.6906 (tp30)
REVERT: D   70 LYS cc_start: 0.8807 (tttt) cc_final: 0.8541 (tppt)
REVERT: E   34 ARG cc_start: 0.8364 (ttt90) cc_final: 0.7538 (pmt-80)
REVERT: E   58 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.6808 (mt)
  outliers start: 16
  outliers final: 14
  residues processed: 120
  average time/residue: 0.1369
  time to fit residues: 20.4030
Evaluate side-chains
  129 residues out of total 395 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 114
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain C residue   82 LEU
Chi-restraints excluded: chain D residue   18 ASP
Chi-restraints excluded: chain D residue   58 LEU
Chi-restraints excluded: chain D residue   68 ILE
Chi-restraints excluded: chain D residue   82 LEU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   58 LEU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   84 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 6 optimal weight:    5.9990
   chunk 31 optimal weight:    6.9990
   chunk 2 optimal weight:   20.0000
   chunk 25 optimal weight:    9.9990
   chunk 40 optimal weight:    0.0570
   chunk 24 optimal weight:   10.0000
   chunk 30 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9980
   chunk 28 optimal weight:   10.0000
   chunk 27 optimal weight:   10.0000
   overall best weight:    3.8104

-------------------------------------------------------------------------------
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 = 0.3771 r_free = 0.3771 target = 0.083852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.075084 restraints weight = 9896.855|
|-----------------------------------------------------------------------------|
r_work (start): 0.3687 rms_B_bonded: 3.75
r_work: 0.3584 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.5271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   3715  Z= 0.318
  Angle     :  0.744   7.439   5055  Z= 0.379
  Chirality :  0.048   0.141    595
  Planarity :  0.003   0.021    625
  Dihedral  :  4.800  20.287    500
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 17.47 %
    Favored  : 78.23 %
  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: -2.79 (0.37), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.12 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP B  79 
 HIS   0.002   0.001   HIS A  31 
 PHE   0.020   0.002   PHE A  33 
 TYR   0.024   0.002   TYR C  69 
 ARG   0.002   0.001   ARG B  34 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1149.50 seconds
wall clock time: 21 minutes 13.66 seconds (1273.66 seconds total)