Starting phenix.real_space_refine
on Tue Mar  3 14:00:09 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cyr_27082/03_2026/8cyr_27082.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cyr_27082/03_2026/8cyr_27082.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cyr_27082/03_2026/8cyr_27082.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cyr_27082/03_2026/8cyr_27082.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8cyr_27082/03_2026/8cyr_27082.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cyr_27082/03_2026/8cyr_27082.map"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 3
    Type Number    sf(0)   Gaussians
     C    3744      2.51       5
     N    1044      2.21       5
     O    1176      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5964
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 497
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 497
          Classifications: {'peptide': 72}
          Link IDs: {'TRANS': 71}
          Chain breaks: 1
  Restraints were copied for chains:
    B, C, D, E, F, I, J, K, L, M, N
  Time building chain proxies: 0.72, per 1000 atoms: 0.12
  Number of scatterers: 5964
  At special positions: 0
  Unit cell: (124.2, 82.08, 51.84, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O    1176      8.00
     N    1044      7.00
     C    3744      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: 0.41
  Conformation dependent library (CDL) restraints added in 371.3 milliseconds
  

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1488

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 18 sheets defined
      0.0% alpha, 34.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 16 through 18
      removed outlier: 6.193A  pdb=" N   ALA C  17 " --> pdb=" O   ALA E  18 " (cutoff:3.500A)
      removed outlier: 6.192A  pdb=" N   ALA A  17 " --> pdb=" O   ALA I  18 " (cutoff:3.500A)
      removed outlier: 6.192A  pdb=" N   ALA I  17 " --> pdb=" O   ALA K  18 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   ALA K  17 " --> pdb=" O   ALA M  18 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 21 through 23
      removed outlier: 6.361A  pdb=" N   THR A  22 " --> pdb=" O   LYS E  23 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 37 through 45
      removed outlier: 6.514A  pdb=" N   VAL A  37 " --> pdb=" O   LEU E  38 " (cutoff:3.500A)
      removed outlier: 7.682A  pdb=" N   VAL E  40 " --> pdb=" O   VAL A  37 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   TYR A  39 " --> pdb=" O   VAL E  40 " (cutoff:3.500A)
      removed outlier: 8.094A  pdb=" N   SER E  42 " --> pdb=" O   TYR A  39 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   GLY A  41 " --> pdb=" O   SER E  42 " (cutoff:3.500A)
      removed outlier: 7.557A  pdb=" N   THR E  44 " --> pdb=" O   GLY A  41 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   LYS A  43 " --> pdb=" O   THR E  44 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 48 through 50
      removed outlier: 6.472A  pdb=" N   VAL A  48 " --> pdb=" O   VAL E  49 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 53 through 55
      removed outlier: 6.071A  pdb=" N   THR C  54 " --> pdb=" O   VAL E  55 " (cutoff:3.500A)
      removed outlier: 6.071A  pdb=" N   THR A  54 " --> pdb=" O   VAL I  55 " (cutoff:3.500A)
      removed outlier: 6.070A  pdb=" N   THR I  54 " --> pdb=" O   VAL K  55 " (cutoff:3.500A)
      removed outlier: 6.071A  pdb=" N   THR K  54 " --> pdb=" O   VAL M  55 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 63 through 66
      removed outlier: 6.788A  pdb=" N   VAL A  63 " --> pdb=" O   THR E  64 " (cutoff:3.500A)
      removed outlier: 7.805A  pdb=" N   VAL E  66 " --> pdb=" O   VAL A  63 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   ASN A  65 " --> pdb=" O   VAL E  66 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 71 through 72
      removed outlier: 6.584A  pdb=" N   VAL A  71 " --> pdb=" O   THR E  72 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 75 through 77
      removed outlier: 6.495A  pdb=" N   ALA A  76 " --> pdb=" O   VAL E  77 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 86 through 88
      removed outlier: 6.251A  pdb=" N   SER C  87 " --> pdb=" O   ILE E  88 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   SER A  87 " --> pdb=" O   ILE I  88 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   SER I  87 " --> pdb=" O   ILE K  88 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   SER K  87 " --> pdb=" O   ILE M  88 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 16 through 18
      removed outlier: 6.322A  pdb=" N   ALA D  17 " --> pdb=" O   ALA F  18 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   ALA B  17 " --> pdb=" O   ALA J  18 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   ALA J  17 " --> pdb=" O   ALA L  18 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   ALA L  17 " --> pdb=" O   ALA N  18 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 21 through 23
      removed outlier: 6.210A  pdb=" N   THR B  22 " --> pdb=" O   LYS F  23 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 37 through 45
      removed outlier: 6.106A  pdb=" N   LEU D  38 " --> pdb=" O   TYR F  39 " (cutoff:3.500A)
      removed outlier: 7.469A  pdb=" N   GLY F  41 " --> pdb=" O   LEU D  38 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   VAL D  40 " --> pdb=" O   GLY F  41 " (cutoff:3.500A)
      removed outlier: 7.879A  pdb=" N   LYS F  43 " --> pdb=" O   VAL D  40 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   SER D  42 " --> pdb=" O   LYS F  43 " (cutoff:3.500A)
      removed outlier: 8.079A  pdb=" N   LYS F  45 " --> pdb=" O   SER D  42 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   THR D  44 " --> pdb=" O   LYS F  45 " (cutoff:3.500A)
      removed outlier: 6.105A  pdb=" N   LEU B  38 " --> pdb=" O   TYR J  39 " (cutoff:3.500A)
      removed outlier: 7.469A  pdb=" N   GLY J  41 " --> pdb=" O   LEU B  38 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   VAL B  40 " --> pdb=" O   GLY J  41 " (cutoff:3.500A)
      removed outlier: 7.879A  pdb=" N   LYS J  43 " --> pdb=" O   VAL B  40 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   SER B  42 " --> pdb=" O   LYS J  43 " (cutoff:3.500A)
      removed outlier: 8.079A  pdb=" N   LYS J  45 " --> pdb=" O   SER B  42 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   THR B  44 " --> pdb=" O   LYS J  45 " (cutoff:3.500A)
      removed outlier: 6.105A  pdb=" N   LEU J  38 " --> pdb=" O   TYR L  39 " (cutoff:3.500A)
      removed outlier: 7.470A  pdb=" N   GLY L  41 " --> pdb=" O   LEU J  38 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   VAL J  40 " --> pdb=" O   GLY L  41 " (cutoff:3.500A)
      removed outlier: 7.879A  pdb=" N   LYS L  43 " --> pdb=" O   VAL J  40 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   SER J  42 " --> pdb=" O   LYS L  43 " (cutoff:3.500A)
      removed outlier: 8.079A  pdb=" N   LYS L  45 " --> pdb=" O   SER J  42 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   THR J  44 " --> pdb=" O   LYS L  45 " (cutoff:3.500A)
      removed outlier: 6.105A  pdb=" N   LEU L  38 " --> pdb=" O   TYR N  39 " (cutoff:3.500A)
      removed outlier: 7.470A  pdb=" N   GLY N  41 " --> pdb=" O   LEU L  38 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   VAL L  40 " --> pdb=" O   GLY N  41 " (cutoff:3.500A)
      removed outlier: 7.878A  pdb=" N   LYS N  43 " --> pdb=" O   VAL L  40 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   SER L  42 " --> pdb=" O   LYS N  43 " (cutoff:3.500A)
      removed outlier: 8.080A  pdb=" N   LYS N  45 " --> pdb=" O   SER L  42 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   THR L  44 " --> pdb=" O   LYS N  45 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 48 through 50
      removed outlier: 6.352A  pdb=" N   VAL B  48 " --> pdb=" O   VAL F  49 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 53 through 55
      removed outlier: 5.829A  pdb=" N   THR D  54 " --> pdb=" O   VAL F  55 " (cutoff:3.500A)
      removed outlier: 5.828A  pdb=" N   THR B  54 " --> pdb=" O   VAL J  55 " (cutoff:3.500A)
      removed outlier: 5.828A  pdb=" N   THR J  54 " --> pdb=" O   VAL L  55 " (cutoff:3.500A)
      removed outlier: 5.829A  pdb=" N   THR L  54 " --> pdb=" O   VAL N  55 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 61 through 66
      removed outlier: 7.027A  pdb=" N   GLU B  61 " --> pdb=" O   GLN F  62 " (cutoff:3.500A)
      removed outlier: 8.570A  pdb=" N   THR F  64 " --> pdb=" O   GLU B  61 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   VAL B  63 " --> pdb=" O   THR F  64 " (cutoff:3.500A)
      removed outlier: 7.574A  pdb=" N   VAL F  66 " --> pdb=" O   VAL B  63 " (cutoff:3.500A)
      removed outlier: 6.182A  pdb=" N   ASN B  65 " --> pdb=" O   VAL F  66 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 71 through 72
      removed outlier: 6.778A  pdb=" N   VAL B  71 " --> pdb=" O   THR F  72 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 75 through 77
      removed outlier: 6.245A  pdb=" N   ALA B  76 " --> pdb=" O   VAL F  77 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 86 through 88
      removed outlier: 6.098A  pdb=" N   SER D  87 " --> pdb=" O   ILE F  88 " (cutoff:3.500A)
      removed outlier: 6.097A  pdb=" N   SER B  87 " --> pdb=" O   ILE J  88 " (cutoff:3.500A)
      removed outlier: 6.097A  pdb=" N   SER J  87 " --> pdb=" O   ILE L  88 " (cutoff:3.500A)
      removed outlier: 6.097A  pdb=" N   SER L  87 " --> pdb=" O   ILE N  88 " (cutoff:3.500A)

    140 hydrogen bonds defined for protein.
    420 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: 0.89

  Time building geometry restraints manager: 0.59 seconds

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

  Histogram of bond lengths:
        1.23 -     1.29: 1032
        1.29 -     1.36: 924
        1.36 -     1.42: 204
        1.42 -     1.48: 972
        1.48 -     1.55: 2844
  Bond restraints: 5976
  Sorted by residual:
  bond pdb=" CA  GLY M  68 "
       pdb=" C   GLY M  68 "
    ideal  model  delta    sigma   weight residual
    1.522  1.508  0.014 1.06e-02 8.90e+03 1.75e+00
  bond pdb=" CA  GLY L  68 "
       pdb=" C   GLY L  68 "
    ideal  model  delta    sigma   weight residual
    1.522  1.508  0.014 1.06e-02 8.90e+03 1.71e+00
  bond pdb=" CA  GLY I  68 "
       pdb=" C   GLY I  68 "
    ideal  model  delta    sigma   weight residual
    1.522  1.508  0.014 1.06e-02 8.90e+03 1.65e+00
  bond pdb=" CA  GLY D  68 "
       pdb=" C   GLY D  68 "
    ideal  model  delta    sigma   weight residual
    1.522  1.508  0.014 1.06e-02 8.90e+03 1.65e+00
  bond pdb=" CA  GLY C  68 "
       pdb=" C   GLY C  68 "
    ideal  model  delta    sigma   weight residual
    1.522  1.508  0.013 1.06e-02 8.90e+03 1.62e+00
  ... (remaining 5971 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.11: 7575
        1.11 -     2.23: 357
        2.23 -     3.34: 96
        3.34 -     4.45: 12
        4.45 -     5.57: 12
  Bond angle restraints: 8052
  Sorted by residual:
  angle pdb=" N   GLY B  73 "
        pdb=" CA  GLY B  73 "
        pdb=" C   GLY B  73 "
      ideal   model   delta    sigma   weight residual
     110.63  116.20   -5.57 1.45e+00 4.76e-01 1.47e+01
  angle pdb=" N   GLY N  73 "
        pdb=" CA  GLY N  73 "
        pdb=" C   GLY N  73 "
      ideal   model   delta    sigma   weight residual
     110.63  116.19   -5.56 1.45e+00 4.76e-01 1.47e+01
  angle pdb=" N   GLY I  73 "
        pdb=" CA  GLY I  73 "
        pdb=" C   GLY I  73 "
      ideal   model   delta    sigma   weight residual
     110.63  116.18   -5.55 1.45e+00 4.76e-01 1.46e+01
  angle pdb=" N   GLY L  73 "
        pdb=" CA  GLY L  73 "
        pdb=" C   GLY L  73 "
      ideal   model   delta    sigma   weight residual
     110.63  116.17   -5.54 1.45e+00 4.76e-01 1.46e+01
  angle pdb=" N   GLY A  73 "
        pdb=" CA  GLY A  73 "
        pdb=" C   GLY A  73 "
      ideal   model   delta    sigma   weight residual
     110.63  116.15   -5.52 1.45e+00 4.76e-01 1.45e+01
  ... (remaining 8047 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     7.22: 3011
        7.22 -    14.44: 289
       14.44 -    21.66: 144
       21.66 -    28.88: 60
       28.88 -    36.09: 24
  Dihedral angle restraints: 3528
    sinusoidal: 1188
      harmonic: 2340
  Sorted by residual:
  dihedral pdb=" N   VAL N  15 "
           pdb=" CA  VAL N  15 "
           pdb=" CB  VAL N  15 "
           pdb=" CG1 VAL N  15 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -143.91  -36.09     3      1.50e+01 4.44e-03 6.23e+00
  dihedral pdb=" N   VAL A  15 "
           pdb=" CA  VAL A  15 "
           pdb=" CB  VAL A  15 "
           pdb=" CG1 VAL A  15 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -143.92  -36.08     3      1.50e+01 4.44e-03 6.22e+00
  dihedral pdb=" N   VAL C  15 "
           pdb=" CA  VAL C  15 "
           pdb=" CB  VAL C  15 "
           pdb=" CG1 VAL C  15 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -143.93  -36.07     3      1.50e+01 4.44e-03 6.22e+00
  ... (remaining 3525 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 458
       0.024 -    0.048: 270
       0.048 -    0.072: 148
       0.072 -    0.096: 28
       0.096 -    0.120: 164
  Chirality restraints: 1068
  Sorted by residual:
  chirality pdb=" CA  ILE K  88 "
            pdb=" N   ILE K  88 "
            pdb=" C   ILE K  88 "
            pdb=" CB  ILE K  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.63e-01
  chirality pdb=" CA  ILE L  88 "
            pdb=" N   ILE L  88 "
            pdb=" C   ILE L  88 "
            pdb=" CB  ILE L  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.60e-01
  chirality pdb=" CA  ILE A  88 "
            pdb=" N   ILE A  88 "
            pdb=" C   ILE A  88 "
            pdb=" CB  ILE A  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.58e-01
  ... (remaining 1065 not shown)

  Planarity restraints: 984
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B  19 "   -0.003 2.00e-02 2.50e+03   5.88e-03 3.46e-01
        pdb=" C   ALA B  19 "    0.010 2.00e-02 2.50e+03
        pdb=" O   ALA B  19 "   -0.004 2.00e-02 2.50e+03
        pdb=" N   GLU B  20 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A  19 "    0.003 2.00e-02 2.50e+03   5.84e-03 3.42e-01
        pdb=" C   ALA A  19 "   -0.010 2.00e-02 2.50e+03
        pdb=" O   ALA A  19 "    0.004 2.00e-02 2.50e+03
        pdb=" N   GLU A  20 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA F  19 "   -0.003 2.00e-02 2.50e+03   5.84e-03 3.41e-01
        pdb=" C   ALA F  19 "    0.010 2.00e-02 2.50e+03
        pdb=" O   ALA F  19 "   -0.004 2.00e-02 2.50e+03
        pdb=" N   GLU F  20 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 981 not shown)

  Histogram of nonbonded interaction distances:
        2.65 -     3.10: 3919
        3.10 -     3.55: 5594
        3.55 -     4.00: 8726
        4.00 -     4.45: 9048
        4.45 -     4.90: 20137
  Nonbonded interactions: 47424
  Sorted by model distance:
  nonbonded pdb=" O   ALA J  17 "
            pdb=" OG  SER L  87 "
     model   vdw
     2.654 3.040
  nonbonded pdb=" O   ALA B  17 "
            pdb=" OG  SER J  87 "
     model   vdw
     2.655 3.040
  nonbonded pdb=" O   ALA L  17 "
            pdb=" OG  SER N  87 "
     model   vdw
     2.655 3.040
  nonbonded pdb=" O   ALA D  17 "
            pdb=" OG  SER F  87 "
     model   vdw
     2.655 3.040
  nonbonded pdb=" OG  SER B  87 "
            pdb=" O   ALA F  17 "
     model   vdw
     2.656 3.040
  ... (remaining 47419 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
  selection = chain 'M'
  selection = chain 'N'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.110
  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:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.770
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5621
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   0.017   5976  Z= 0.172
  Angle     :  0.625   5.568   8052  Z= 0.402
  Chirality :  0.054   0.120   1068
  Planarity :  0.002   0.006    984
  Dihedral  :  8.968  36.094   2040
  Min Nonbonded Distance : 2.654

Molprobity Statistics.
  All-atom Clashscore : 0.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  :  4.00 %
    Favored  : 94.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.37 (0.26), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.80 (0.20), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR D  39 
 PHE   0.004   0.001   PHE E  94 
 HIS   0.001   0.000   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 5976)
  covalent geometry    : angle       0.62463 ( 8052)
  hydrogen bonds       : bond        0.14885 (  140)
  hydrogen bonds       : angle       8.94482 (  420)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 199
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   15 VAL cc_start: 0.6713 (OUTLIER) cc_final: 0.5593 (t)
REVERT: D   15 VAL cc_start: 0.7419 (OUTLIER) cc_final: 0.6550 (t)
REVERT: F   15 VAL cc_start: 0.7013 (OUTLIER) cc_final: 0.6061 (t)
REVERT: I   15 VAL cc_start: 0.5408 (OUTLIER) cc_final: 0.5192 (t)
REVERT: J   15 VAL cc_start: 0.7263 (OUTLIER) cc_final: 0.6373 (t)
REVERT: K   15 VAL cc_start: 0.5777 (OUTLIER) cc_final: 0.5315 (t)
REVERT: L   38 LEU cc_start: 0.7526 (mp) cc_final: 0.6891 (mp)
REVERT: L   72 THR cc_start: 0.7717 (m) cc_final: 0.7404 (t)
REVERT: L   79 GLN cc_start: 0.7377 (mt0) cc_final: 0.7116 (mt0)
REVERT: N   39 TYR cc_start: 0.6987 (t80) cc_final: 0.6636 (t80)
  outliers start: 12
  outliers final: 2
  residues processed: 210
  average time/residue: 0.1074
  time to fit residues: 27.6550
Evaluate side-chains
  76 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 68
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:   20.0000
   chunk 53 optimal weight:    0.0970
   chunk 5 optimal weight:   20.0000
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:   30.0000
   chunk 62 optimal weight:   20.0000
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:   20.0000
   chunk 61 optimal weight:   20.0000
   chunk 45 optimal weight:   30.0000
   chunk 74 optimal weight:    0.7980
   overall best weight:    6.1786

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

Flipped N/Q/H residues before XYZ refinement:
** B  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  62 GLN
** F  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4591 r_free = 0.4591 target = 0.184525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.154937 restraints weight = 11176.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.156897 restraints weight = 8977.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.158301 restraints weight = 7630.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.159103 restraints weight = 6774.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.159825 restraints weight = 6282.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.4326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6533
moved from start:          0.4841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   5976  Z= 0.246
  Angle     :  0.665   7.322   8052  Z= 0.372
  Chirality :  0.054   0.157   1068
  Planarity :  0.003   0.013    984
  Dihedral  :  5.141  22.469    852
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  3.17 %
    Favored  : 96.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.21 (0.28), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.68 (0.21), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.018   0.003   TYR N  39 
 PHE   0.013   0.002   PHE E  94 
 HIS   0.004   0.001   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 ( 5976)
  covalent geometry    : angle       0.66541 ( 8052)
  hydrogen bonds       : bond        0.03578 (  140)
  hydrogen bonds       : angle       5.78321 (  420)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 106
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   46 GLU cc_start: 0.8468 (tt0) cc_final: 0.8051 (tt0)
REVERT: E   46 GLU cc_start: 0.8391 (tt0) cc_final: 0.7520 (tm-30)
REVERT: E   72 THR cc_start: 0.7604 (m) cc_final: 0.7329 (p)
REVERT: F   39 TYR cc_start: 0.7402 (t80) cc_final: 0.7115 (t80)
REVERT: J   83 GLU cc_start: 0.7020 (tt0) cc_final: 0.6727 (tt0)
REVERT: M   59 THR cc_start: 0.3542 (p) cc_final: 0.3122 (p)
REVERT: M   80 LYS cc_start: 0.8164 (mmmt) cc_final: 0.6691 (pttp)
  outliers start: 2
  outliers final: 0
  residues processed: 107
  average time/residue: 0.1040
  time to fit residues: 13.8984
Evaluate side-chains
  64 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 58 optimal weight:   30.0000
   chunk 40 optimal weight:    2.9990
   chunk 61 optimal weight:   20.0000
   chunk 44 optimal weight:    9.9990
   chunk 65 optimal weight:    8.9990
   chunk 28 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 72 optimal weight:    8.9990
   chunk 3 optimal weight:    8.9990
   chunk 62 optimal weight:   40.0000
   chunk 17 optimal weight:    8.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  62 GLN
** B  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4553 r_free = 0.4553 target = 0.179136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.151882 restraints weight = 11024.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.153786 restraints weight = 8606.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.155187 restraints weight = 7212.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.156058 restraints weight = 6336.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.156667 restraints weight = 5805.311|
|-----------------------------------------------------------------------------|
r_work (final): 0.4292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6657
moved from start:          0.6081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   5976  Z= 0.189
  Angle     :  0.583  11.265   8052  Z= 0.326
  Chirality :  0.052   0.134   1068
  Planarity :  0.003   0.018    984
  Dihedral  :  4.973  19.152    852
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  4.17 %
    Favored  : 95.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.52 (0.26), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.91 (0.20), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.012   0.002   TYR D  39 
 PHE   0.009   0.002   PHE D  94 
 HIS   0.003   0.001   HIS I  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 5976)
  covalent geometry    : angle       0.58278 ( 8052)
  hydrogen bonds       : bond        0.03382 (  140)
  hydrogen bonds       : angle       5.13756 (  420)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 98
  time to evaluate  : 0.218 
Fit side-chains
REVERT: B   38 LEU cc_start: 0.8612 (mp) cc_final: 0.8306 (mp)
REVERT: C   46 GLU cc_start: 0.8532 (tt0) cc_final: 0.8233 (tt0)
REVERT: C   80 LYS cc_start: 0.5035 (mmpt) cc_final: 0.4677 (mmmt)
REVERT: E   46 GLU cc_start: 0.8434 (tt0) cc_final: 0.7436 (tm-30)
REVERT: J   63 VAL cc_start: 0.8745 (t) cc_final: 0.8504 (m)
REVERT: L   62 GLN cc_start: 0.7249 (pm20) cc_final: 0.6902 (pm20)
REVERT: M   46 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7792 (tm-30)
REVERT: M   62 GLN cc_start: 0.4227 (pm20) cc_final: 0.3762 (pm20)
REVERT: M   80 LYS cc_start: 0.8321 (mmmt) cc_final: 0.6831 (pttp)
REVERT: N   44 THR cc_start: 0.6901 (p) cc_final: 0.6511 (m)
  outliers start: 1
  outliers final: 1
  residues processed: 99
  average time/residue: 0.0946
  time to fit residues: 12.0675
Evaluate side-chains
  71 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 70
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:   20.0000
   chunk 43 optimal weight:   30.0000
   chunk 48 optimal weight:   30.0000
   chunk 9 optimal weight:    6.9990
   chunk 75 optimal weight:   20.0000
   chunk 12 optimal weight:    2.9990
   chunk 60 optimal weight:    9.9990
   chunk 8 optimal weight:   20.0000
   chunk 16 optimal weight:    0.9980
   chunk 42 optimal weight:    9.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    4.3988

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

Flipped N/Q/H residues before XYZ refinement:
A  62 GLN
** B  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  62 GLN
** F  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4553 r_free = 0.4553 target = 0.178119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.152431 restraints weight = 11311.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.154230 restraints weight = 8705.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.155673 restraints weight = 7246.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.156520 restraints weight = 6324.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.157256 restraints weight = 5766.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.4302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6676
moved from start:          0.6620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5976  Z= 0.147
  Angle     :  0.529   8.714   8052  Z= 0.296
  Chirality :  0.051   0.135   1068
  Planarity :  0.002   0.018    984
  Dihedral  :  4.590  16.358    852
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.67 (0.26), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.03 (0.20), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.010   0.002   TYR B  39 
 PHE   0.006   0.001   PHE E  94 
 HIS   0.002   0.000   HIS L  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 5976)
  covalent geometry    : angle       0.52893 ( 8052)
  hydrogen bonds       : bond        0.03152 (  140)
  hydrogen bonds       : angle       4.75429 (  420)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.216 
Fit side-chains
REVERT: C   46 GLU cc_start: 0.8614 (tt0) cc_final: 0.8266 (tt0)
REVERT: D   61 GLU cc_start: 0.3740 (pt0) cc_final: 0.3436 (pt0)
REVERT: E   46 GLU cc_start: 0.8442 (tt0) cc_final: 0.7486 (tm-30)
REVERT: F   83 GLU cc_start: 0.6213 (tp30) cc_final: 0.6009 (tp30)
REVERT: J   57 GLU cc_start: 0.4038 (tm-30) cc_final: 0.3022 (tm-30)
REVERT: K   62 GLN cc_start: 0.6138 (pm20) cc_final: 0.5750 (pm20)
REVERT: M   46 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7814 (tm-30)
REVERT: M   80 LYS cc_start: 0.8178 (mmmt) cc_final: 0.6844 (pttp)
REVERT: N   44 THR cc_start: 0.7187 (p) cc_final: 0.6810 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.0807
  time to fit residues: 10.6114
Evaluate side-chains
  73 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 71 optimal weight:    0.0570
   chunk 67 optimal weight:    2.9990
   chunk 27 optimal weight:    7.9990
   chunk 19 optimal weight:   10.0000
   chunk 51 optimal weight:    5.9990
   chunk 79 optimal weight:    0.6980
   chunk 54 optimal weight:   20.0000
   chunk 0 optimal weight:   50.0000
   chunk 29 optimal weight:   30.0000
   chunk 53 optimal weight:    6.9990
   chunk 2 optimal weight:   30.0000
   overall best weight:    3.3504

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

Flipped N/Q/H residues before XYZ refinement:
** B  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4577 r_free = 0.4577 target = 0.179207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.153221 restraints weight = 11649.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.155292 restraints weight = 8972.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.156718 restraints weight = 7411.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.157775 restraints weight = 6432.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.158314 restraints weight = 5801.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.4318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6672
moved from start:          0.6905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5976  Z= 0.126
  Angle     :  0.520   7.670   8052  Z= 0.288
  Chirality :  0.051   0.151   1068
  Planarity :  0.002   0.012    984
  Dihedral  :  4.406  14.171    852
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.61 (0.26), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.98 (0.20), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.009   0.001   TYR D  39 
 PHE   0.007   0.001   PHE D  94 
 HIS   0.001   0.000   HIS I  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 5976)
  covalent geometry    : angle       0.51962 ( 8052)
  hydrogen bonds       : bond        0.02897 (  140)
  hydrogen bonds       : angle       4.60031 (  420)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
REVERT: B   57 GLU cc_start: 0.4148 (tp30) cc_final: 0.3925 (tp30)
REVERT: B   92 THR cc_start: 0.8044 (t) cc_final: 0.7669 (m)
REVERT: C   46 GLU cc_start: 0.8587 (tt0) cc_final: 0.8183 (tt0)
REVERT: D   61 GLU cc_start: 0.3923 (pt0) cc_final: 0.3619 (pt0)
REVERT: E   46 GLU cc_start: 0.8450 (tt0) cc_final: 0.7570 (tm-30)
REVERT: L   62 GLN cc_start: 0.7216 (pm20) cc_final: 0.6944 (pm20)
REVERT: M   46 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7833 (tm-30)
REVERT: M   80 LYS cc_start: 0.8285 (mmmt) cc_final: 0.6840 (pttp)
REVERT: N   44 THR cc_start: 0.7180 (p) cc_final: 0.6802 (m)
REVERT: N   80 LYS cc_start: 0.4001 (pptt) cc_final: 0.3454 (pptt)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.0836
  time to fit residues: 10.4027
Evaluate side-chains
  70 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 3 optimal weight:    8.9990
   chunk 10 optimal weight:   30.0000
   chunk 0 optimal weight:   50.0000
   chunk 11 optimal weight:    0.9990
   chunk 22 optimal weight:    7.9990
   chunk 62 optimal weight:   30.0000
   chunk 40 optimal weight:    0.8980
   chunk 1 optimal weight:   30.0000
   chunk 73 optimal weight:    7.9990
   chunk 26 optimal weight:    8.9990
   chunk 45 optimal weight:    6.9990
   overall best weight:    4.9788

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

Flipped N/Q/H residues before XYZ refinement:
** B  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4539 r_free = 0.4539 target = 0.174649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.150585 restraints weight = 11669.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.152300 restraints weight = 8978.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.153692 restraints weight = 7502.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.154501 restraints weight = 6541.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.155189 restraints weight = 5956.855|
|-----------------------------------------------------------------------------|
r_work (final): 0.4295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6740
moved from start:          0.7359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5976  Z= 0.161
  Angle     :  0.563   7.594   8052  Z= 0.312
  Chirality :  0.052   0.157   1068
  Planarity :  0.002   0.011    984
  Dihedral  :  4.765  17.190    852
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.70 (0.25), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.05 (0.19), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.015   0.002   TYR D  39 
 PHE   0.007   0.001   PHE A  94 
 HIS   0.002   0.001   HIS L  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 5976)
  covalent geometry    : angle       0.56263 ( 8052)
  hydrogen bonds       : bond        0.03278 (  140)
  hydrogen bonds       : angle       4.67347 (  420)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   57 GLU cc_start: 0.4846 (tp30) cc_final: 0.4275 (tp30)
REVERT: C   46 GLU cc_start: 0.8570 (tt0) cc_final: 0.8160 (tt0)
REVERT: D   61 GLU cc_start: 0.4068 (pt0) cc_final: 0.3847 (pt0)
REVERT: E   46 GLU cc_start: 0.8415 (tt0) cc_final: 0.7615 (tm-30)
REVERT: F   83 GLU cc_start: 0.6355 (tp30) cc_final: 0.5922 (tp30)
REVERT: K   46 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7754 (tm-30)
REVERT: K   62 GLN cc_start: 0.5372 (pm20) cc_final: 0.4958 (pm20)
REVERT: K   80 LYS cc_start: 0.8836 (mmmm) cc_final: 0.8515 (mmtt)
REVERT: L   62 GLN cc_start: 0.7218 (pm20) cc_final: 0.7007 (pm20)
REVERT: M   46 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7925 (tm-30)
REVERT: M   80 LYS cc_start: 0.8253 (mmmt) cc_final: 0.6962 (pttp)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.0893
  time to fit residues: 10.9375
Evaluate side-chains
  74 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 82 optimal weight:    9.9990
   chunk 45 optimal weight:    0.7980
   chunk 24 optimal weight:    5.9990
   chunk 19 optimal weight:    8.9990
   chunk 10 optimal weight:    9.9990
   chunk 27 optimal weight:    9.9990
   chunk 15 optimal weight:    9.9990
   chunk 61 optimal weight:   20.0000
   chunk 60 optimal weight:    0.0050
   chunk 18 optimal weight:    6.9990
   chunk 29 optimal weight:   10.0000
   overall best weight:    4.5600

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

Flipped N/Q/H residues before XYZ refinement:
** B  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4533 r_free = 0.4533 target = 0.174201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.149694 restraints weight = 11329.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.151769 restraints weight = 8539.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.153226 restraints weight = 6965.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.154081 restraints weight = 5986.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.154845 restraints weight = 5423.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.4286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6756
moved from start:          0.7773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5976  Z= 0.144
  Angle     :  0.549   8.839   8052  Z= 0.306
  Chirality :  0.052   0.147   1068
  Planarity :  0.002   0.011    984
  Dihedral  :  4.750  16.795    852
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.78 (0.25), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.11 (0.19), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.015   0.002   TYR B  39 
 PHE   0.006   0.001   PHE E  94 
 HIS   0.003   0.001   HIS I  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 5976)
  covalent geometry    : angle       0.54876 ( 8052)
  hydrogen bonds       : bond        0.03047 (  140)
  hydrogen bonds       : angle       4.65930 (  420)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   46 GLU cc_start: 0.8491 (tt0) cc_final: 0.8074 (tt0)
REVERT: D   61 GLU cc_start: 0.4344 (pt0) cc_final: 0.4040 (pt0)
REVERT: E   20 GLU cc_start: 0.7486 (mp0) cc_final: 0.7218 (mp0)
REVERT: E   46 GLU cc_start: 0.8407 (tt0) cc_final: 0.7602 (tm-30)
REVERT: K   46 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7661 (tm-30)
REVERT: K   80 LYS cc_start: 0.8786 (mmmm) cc_final: 0.8541 (mmtt)
REVERT: M   46 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7634 (tm-30)
REVERT: M   80 LYS cc_start: 0.8241 (mmmt) cc_final: 0.6963 (pttp)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.0761
  time to fit residues: 10.1417
Evaluate side-chains
  77 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 82 optimal weight:    8.9990
   chunk 4 optimal weight:    6.9990
   chunk 8 optimal weight:   20.0000
   chunk 18 optimal weight:    0.0170
   chunk 70 optimal weight:   20.0000
   chunk 68 optimal weight:    4.9990
   chunk 48 optimal weight:   40.0000
   chunk 37 optimal weight:    7.9990
   chunk 28 optimal weight:   40.0000
   chunk 75 optimal weight:    9.9990
   chunk 67 optimal weight:    6.9990
   overall best weight:    5.4026

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

Flipped N/Q/H residues before XYZ refinement:
** B  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4542 r_free = 0.4542 target = 0.174058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.149548 restraints weight = 11768.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.151474 restraints weight = 8813.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.152868 restraints weight = 7221.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.153816 restraints weight = 6258.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.154538 restraints weight = 5652.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.4276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6793
moved from start:          0.8089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5976  Z= 0.164
  Angle     :  0.577   7.441   8052  Z= 0.318
  Chirality :  0.053   0.160   1068
  Planarity :  0.002   0.012    984
  Dihedral  :  4.965  19.399    852
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.87 (0.24), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.18 (0.19), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.015   0.002   TYR D  39 
 PHE   0.007   0.001   PHE E  94 
 HIS   0.002   0.001   HIS L  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 5976)
  covalent geometry    : angle       0.57684 ( 8052)
  hydrogen bonds       : bond        0.03238 (  140)
  hydrogen bonds       : angle       4.78066 (  420)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
REVERT: B   38 LEU cc_start: 0.8547 (mp) cc_final: 0.8308 (mp)
REVERT: B   83 GLU cc_start: 0.7172 (tp30) cc_final: 0.6963 (tp30)
REVERT: D   61 GLU cc_start: 0.4534 (pt0) cc_final: 0.4252 (pt0)
REVERT: F   83 GLU cc_start: 0.6425 (tp30) cc_final: 0.6057 (tp30)
REVERT: K   46 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7699 (tm-30)
REVERT: K   62 GLN cc_start: 0.5806 (pm20) cc_final: 0.5474 (pm20)
REVERT: K   80 LYS cc_start: 0.8760 (mmmm) cc_final: 0.8375 (mmtt)
REVERT: L   45 LYS cc_start: 0.7969 (mtpt) cc_final: 0.7287 (mttp)
REVERT: M   46 GLU cc_start: 0.8348 (tm-30) cc_final: 0.7614 (tm-30)
REVERT: M   80 LYS cc_start: 0.8285 (mmmt) cc_final: 0.6996 (pttp)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.0807
  time to fit residues: 11.0500
Evaluate side-chains
  78 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 64 optimal weight:   10.0000
   chunk 82 optimal weight:    0.8980
   chunk 25 optimal weight:    6.9990
   chunk 72 optimal weight:    0.7980
   chunk 47 optimal weight:    6.9990
   chunk 13 optimal weight:   40.0000
   chunk 56 optimal weight:   30.0000
   chunk 19 optimal weight:   20.0000
   chunk 40 optimal weight:   20.0000
   chunk 24 optimal weight:    0.7980
   chunk 41 optimal weight:   30.0000
   overall best weight:    3.2984

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

Flipped N/Q/H residues before XYZ refinement:
** B  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  62 GLN
** F  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4567 r_free = 0.4567 target = 0.176945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.153636 restraints weight = 11664.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.155477 restraints weight = 8847.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.156750 restraints weight = 7349.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.157540 restraints weight = 6373.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.158190 restraints weight = 5806.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.4312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6740
moved from start:          0.8147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5976  Z= 0.121
  Angle     :  0.549   7.170   8052  Z= 0.304
  Chirality :  0.053   0.167   1068
  Planarity :  0.002   0.011    984
  Dihedral  :  4.640  15.468    852
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.17 %
    Favored  : 99.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.78 (0.25), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.11 (0.19), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.013   0.002   TYR F  39 
 PHE   0.005   0.001   PHE E  94 
 HIS   0.001   0.000   HIS I  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 5976)
  covalent geometry    : angle       0.54947 ( 8052)
  hydrogen bonds       : bond        0.03032 (  140)
  hydrogen bonds       : angle       4.66884 (  420)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
REVERT: D   61 GLU cc_start: 0.4573 (pt0) cc_final: 0.4228 (pt0)
REVERT: E   20 GLU cc_start: 0.7527 (mp0) cc_final: 0.7258 (mp0)
REVERT: K   46 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7696 (tm-30)
REVERT: K   62 GLN cc_start: 0.5840 (pm20) cc_final: 0.5591 (pm20)
REVERT: K   80 LYS cc_start: 0.8798 (mmmm) cc_final: 0.8529 (mmtt)
REVERT: L   45 LYS cc_start: 0.7634 (mtpt) cc_final: 0.7359 (mttp)
REVERT: M   46 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7599 (tm-30)
REVERT: M   80 LYS cc_start: 0.8275 (mmmt) cc_final: 0.6961 (pttp)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.0773
  time to fit residues: 9.8364
Evaluate side-chains
  75 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 42 optimal weight:   20.0000
   chunk 54 optimal weight:    7.9990
   chunk 77 optimal weight:    6.9990
   chunk 23 optimal weight:    6.9990
   chunk 46 optimal weight:   10.0000
   chunk 9 optimal weight:    5.9990
   chunk 4 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9990
   chunk 38 optimal weight:   20.0000
   chunk 19 optimal weight:   20.0000
   chunk 52 optimal weight:    6.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** B  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4534 r_free = 0.4534 target = 0.173182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.150512 restraints weight = 11591.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.152261 restraints weight = 8767.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.153527 restraints weight = 7222.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.154544 restraints weight = 6245.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.154963 restraints weight = 5593.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.4291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6816
moved from start:          0.8491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   5976  Z= 0.167
  Angle     :  0.605   6.924   8052  Z= 0.334
  Chirality :  0.053   0.179   1068
  Planarity :  0.002   0.011    984
  Dihedral  :  5.074  18.128    852
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.60 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.17 %
    Favored  : 99.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.95 (0.24), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.24 (0.18), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.018   0.002   TYR N  39 
 PHE   0.008   0.001   PHE E  94 
 HIS   0.002   0.001   HIS I  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 5976)
  covalent geometry    : angle       0.60512 ( 8052)
  hydrogen bonds       : bond        0.03301 (  140)
  hydrogen bonds       : angle       4.90222 (  420)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.277 
Fit side-chains
REVERT: D   61 GLU cc_start: 0.4917 (pt0) cc_final: 0.4547 (pt0)
REVERT: E   20 GLU cc_start: 0.7518 (mp0) cc_final: 0.7237 (mp0)
REVERT: K   46 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7657 (tm-30)
REVERT: K   80 LYS cc_start: 0.8768 (mmmm) cc_final: 0.8404 (mmtt)
REVERT: L   45 LYS cc_start: 0.7956 (mtpt) cc_final: 0.7239 (mttp)
REVERT: M   46 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7620 (tm-30)
REVERT: M   80 LYS cc_start: 0.8355 (mmmt) cc_final: 0.7031 (pttp)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.0834
  time to fit residues: 10.3005
Evaluate side-chains
  69 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 71 optimal weight:    0.0870
   chunk 76 optimal weight:    9.9990
   chunk 50 optimal weight:   20.0000
   chunk 49 optimal weight:   30.0000
   chunk 42 optimal weight:    8.9990
   chunk 56 optimal weight:    9.9990
   chunk 80 optimal weight:    8.9990
   chunk 13 optimal weight:   40.0000
   chunk 51 optimal weight:   30.0000
   chunk 20 optimal weight:    6.9990
   overall best weight:    5.1764

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

Flipped N/Q/H residues before XYZ refinement:
** B  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4546 r_free = 0.4546 target = 0.174039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.150789 restraints weight = 11474.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.152748 restraints weight = 8535.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.154130 restraints weight = 6926.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.155112 restraints weight = 5944.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.155820 restraints weight = 5324.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.4300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6805
moved from start:          0.8610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5976  Z= 0.156
  Angle     :  0.597   6.419   8052  Z= 0.329
  Chirality :  0.053   0.156   1068
  Planarity :  0.002   0.011    984
  Dihedral  :  5.063  17.891    852
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.35 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.17 %
    Favored  : 99.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.03 (0.24), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.30 (0.18), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.014   0.002   TYR F  39 
 PHE   0.007   0.001   PHE E  94 
 HIS   0.002   0.001   HIS L  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 5976)
  covalent geometry    : angle       0.59715 ( 8052)
  hydrogen bonds       : bond        0.03229 (  140)
  hydrogen bonds       : angle       4.83312 (  420)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 949.73 seconds
wall clock time: 17 minutes 10.94 seconds (1030.94 seconds total)