Starting phenix.real_space_refine
on Thu Mar  6 09:38:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cyr_27082/03_2025/8cyr_27082.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cyr_27082/03_2025/8cyr_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8cyr_27082/03_2025/8cyr_27082.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cyr_27082/03_2025/8cyr_27082.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cyr_27082/03_2025/8cyr_27082.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cyr_27082/03_2025/8cyr_27082.cif"
  }
  resolution = 4.2
  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=   0.002 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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:
    C, B, E, D, F, I, K, J, M, L, N
  Time building chain proxies: 1.81, per 1000 atoms: 0.30
  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: 1.26
  Conformation dependent library (CDL) restraints added in 761.3 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: 1.31
  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: 1.72

  Time building geometry restraints manager: 1.52 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: 0.09
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'K'
  selection = chain 'J'
  selection = chain 'M'
  selection = chain 'L'
  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:             0.130
  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:             0.020
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     15.820
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.020
  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:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.520
-------------------------------------------------------------------------------
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= 0.181
  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 (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 (0.26), 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
 HIS   0.001   0.000   HIS C  50 
 PHE   0.004   0.001   PHE E  94 
 TYR   0.006   0.001   TYR D  39 

*********************** 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  : 0.656 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   15 VAL cc_start: 0.6713 (OUTLIER) cc_final: 0.5594 (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: 0.5193 (t)
REVERT: J   15 VAL cc_start: 0.7262 (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: 0.6892 (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: 0.6986 (t80) cc_final: 0.6636 (t80)
  outliers start: 12
  outliers final: 2
  residues processed: 210
  average time/residue: 0.2315
  time to fit residues: 59.3086
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  : 0.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    5.9990
   chunk 63 optimal weight:   30.0000
   chunk 35 optimal weight:   30.0000
   chunk 21 optimal weight:    5.9990
   chunk 42 optimal weight:   50.0000
   chunk 34 optimal weight:   20.0000
   chunk 65 optimal weight:   30.0000
   chunk 25 optimal weight:   20.0000
   chunk 40 optimal weight:   20.0000
   chunk 49 optimal weight:    6.9990
   chunk 76 optimal weight:    8.9990
   overall best weight:    9.5992

-------------------------------------------------------------------------------
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 = 0.4537 r_free = 0.4537 target = 0.177341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.148779 restraints weight = 11211.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.150559 restraints weight = 8910.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.151586 restraints weight = 7661.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.4229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6695
moved from start:          0.5705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.069   5976  Z= 0.453
  Angle     :  0.801   7.453   8052  Z= 0.446
  Chirality :  0.057   0.170   1068
  Planarity :  0.004   0.018    984
  Dihedral  :  6.393  30.200    852
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  :  5.51 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  4.17 %
    Favored  : 95.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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: -2.45 (0.27), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.86 (0.21), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C  50 
 PHE   0.017   0.003   PHE E  94 
 TYR   0.024   0.004   TYR N  39 

*********************** 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
  111 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 109
  time to evaluate  : 0.679 
Fit side-chains
   revert: symmetry clash
REVERT: C   46 GLU cc_start: 0.8470 (tt0) cc_final: 0.7964 (tt0)
REVERT: E   46 GLU cc_start: 0.8429 (tt0) cc_final: 0.7465 (tm-30)
REVERT: J   45 LYS cc_start: 0.7997 (mtpt) cc_final: 0.7629 (mtpp)
REVERT: J   83 GLU cc_start: 0.7106 (tt0) cc_final: 0.6642 (tt0)
REVERT: J   92 THR cc_start: 0.7642 (p) cc_final: 0.7420 (p)
REVERT: M   43 LYS cc_start: 0.7032 (mmpt) cc_final: 0.6818 (mmmt)
REVERT: M   80 LYS cc_start: 0.8093 (mmmt) cc_final: 0.6675 (pttp)
  outliers start: 2
  outliers final: 0
  residues processed: 110
  average time/residue: 0.2305
  time to fit residues: 31.3592
Evaluate side-chains
  67 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 43 optimal weight:   20.0000
   chunk 82 optimal weight:    4.9990
   chunk 13 optimal weight:    6.9990
   chunk 78 optimal weight:    0.1980
   chunk 34 optimal weight:   10.0000
   chunk 73 optimal weight:    1.9990
   chunk 31 optimal weight:   10.0000
   chunk 77 optimal weight:   10.0000
   chunk 74 optimal weight:    8.9990
   chunk 69 optimal weight:    7.9990
   overall best weight:    2.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  62 GLN
** 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 = 0.4564 r_free = 0.4564 target = 0.181208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.154248 restraints weight = 11089.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.156073 restraints weight = 8433.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.157474 restraints weight = 7009.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.4296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6618
moved from start:          0.5955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5976  Z= 0.183
  Angle     :  0.536  10.496   8052  Z= 0.299
  Chirality :  0.053   0.177   1068
  Planarity :  0.002   0.010    984
  Dihedral  :  4.667  17.487    852
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.42 (0.27), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.84 (0.20), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS I  50 
 PHE   0.007   0.001   PHE D  94 
 TYR   0.009   0.001   TYR D  39 

*********************** 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
  100 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.625 
Fit side-chains
   revert: symmetry clash
REVERT: C   80 LYS cc_start: 0.4950 (mmpt) cc_final: 0.4515 (mmmt)
REVERT: E   46 GLU cc_start: 0.8534 (tt0) cc_final: 0.7534 (tm-30)
REVERT: F   80 LYS cc_start: 0.8256 (mttp) cc_final: 0.8027 (mttt)
REVERT: J   92 THR cc_start: 0.7378 (p) cc_final: 0.6894 (m)
REVERT: L   79 GLN cc_start: 0.8010 (mt0) cc_final: 0.7804 (mt0)
REVERT: M   43 LYS cc_start: 0.7629 (mmpt) cc_final: 0.7413 (mptt)
REVERT: M   80 LYS cc_start: 0.8141 (mmmt) cc_final: 0.6618 (pttp)
REVERT: N   44 THR cc_start: 0.6904 (p) cc_final: 0.6611 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.1984
  time to fit residues: 25.3796
Evaluate side-chains
  62 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 69 optimal weight:   20.0000
   chunk 61 optimal weight:   20.0000
   chunk 10 optimal weight:    6.9990
   chunk 46 optimal weight:   20.0000
   chunk 50 optimal weight:    0.1980
   chunk 43 optimal weight:   20.0000
   chunk 44 optimal weight:    0.2980
   chunk 52 optimal weight:   20.0000
   chunk 41 optimal weight:    6.9990
   chunk 24 optimal weight:    0.0060
   chunk 57 optimal weight:    8.9990
   overall best weight:    2.9000

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

Flipped N/Q/H residues before XYZ refinement:
** A  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4583 r_free = 0.4583 target = 0.180994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.154813 restraints weight = 11498.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.156775 restraints weight = 8867.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.158191 restraints weight = 7334.222|
|-----------------------------------------------------------------------------|
r_work (final): 0.4313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6634
moved from start:          0.6304

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= 0.183
  Angle     :  0.509   8.526   8052  Z= 0.286
  Chirality :  0.052   0.147   1068
  Planarity :  0.002   0.021    984
  Dihedral  :  4.283  13.792    852
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  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 (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: -2.42 (0.27), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.84 (0.20), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS L  50 
 PHE   0.005   0.001   PHE A  94 
 TYR   0.010   0.001   TYR D  39 

*********************** 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
  96 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.616 
Fit side-chains
REVERT: C   72 THR cc_start: 0.7646 (t) cc_final: 0.7438 (p)
REVERT: E   46 GLU cc_start: 0.8409 (tt0) cc_final: 0.7723 (tm-30)
REVERT: J   45 LYS cc_start: 0.7701 (mtpp) cc_final: 0.7370 (mttt)
REVERT: M   80 LYS cc_start: 0.8250 (mmmt) cc_final: 0.6707 (pttp)
REVERT: N   44 THR cc_start: 0.7051 (p) cc_final: 0.6762 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.1719
  time to fit residues: 21.7465
Evaluate side-chains
  62 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.599 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 2 optimal weight:   30.0000
   chunk 69 optimal weight:   30.0000
   chunk 1 optimal weight:   20.0000
   chunk 6 optimal weight:    9.9990
   chunk 10 optimal weight:   20.0000
   chunk 73 optimal weight:   10.0000
   chunk 12 optimal weight:   20.0000
   chunk 25 optimal weight:    6.9990
   chunk 82 optimal weight:    5.9990
   chunk 42 optimal weight:    0.8980
   chunk 33 optimal weight:   20.0000
   overall best weight:    6.7790

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

Flipped N/Q/H residues before XYZ refinement:
** A  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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**
** K  62 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 = 0.4510 r_free = 0.4510 target = 0.171120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.146441 restraints weight = 11386.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.148319 restraints weight = 8752.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.149701 restraints weight = 7245.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.4228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6764
moved from start:          0.7286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5976  Z= 0.303
  Angle     :  0.639   8.610   8052  Z= 0.355
  Chirality :  0.053   0.159   1068
  Planarity :  0.003   0.019    984
  Dihedral  :  5.465  23.774    852
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.84 %
    Favored  : 92.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.88 (0.25), 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
 HIS   0.003   0.001   HIS L  50 
 PHE   0.009   0.002   PHE D  94 
 TYR   0.015   0.003   TYR D  39 

*********************** 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  : 0.658 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   83 GLU cc_start: 0.6117 (tp30) cc_final: 0.5624 (tp30)
REVERT: J   45 LYS cc_start: 0.7964 (mtpt) cc_final: 0.7658 (mttt)
REVERT: K   60 LYS cc_start: 0.6783 (tttt) cc_final: 0.6313 (tttt)
REVERT: M   46 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7648 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.2057
  time to fit residues: 25.9640
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  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 17 optimal weight:   40.0000
   chunk 47 optimal weight:   20.0000
   chunk 48 optimal weight:   20.0000
   chunk 76 optimal weight:   20.0000
   chunk 2 optimal weight:   30.0000
   chunk 12 optimal weight:   10.0000
   chunk 44 optimal weight:    7.9990
   chunk 70 optimal weight:   10.0000
   chunk 24 optimal weight:    0.3980
   chunk 61 optimal weight:    5.9990
   chunk 40 optimal weight:   10.0000
   overall best weight:    6.8792

-------------------------------------------------------------------------------
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**
** 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 = 0.4516 r_free = 0.4516 target = 0.171293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.145939 restraints weight = 11473.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.147942 restraints weight = 8467.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.149497 restraints weight = 6858.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.4205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6810
moved from start:          0.7826

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= 0.288
  Angle     :  0.638   8.918   8052  Z= 0.351
  Chirality :  0.053   0.149   1068
  Planarity :  0.002   0.015    984
  Dihedral  :  5.427  20.902    852
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 12.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.97 %
    Favored  : 92.03 %
  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 (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: -3.07 (0.24), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.33 (0.18), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS L  50 
 PHE   0.007   0.001   PHE E  94 
 TYR   0.013   0.002   TYR L  39 

*********************** 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
  100 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.654 
Fit side-chains
REVERT: B   83 GLU cc_start: 0.7140 (tp30) cc_final: 0.6855 (tp30)
REVERT: E   20 GLU cc_start: 0.7491 (mp0) cc_final: 0.7222 (mp0)
REVERT: E   46 GLU cc_start: 0.8491 (tt0) cc_final: 0.7086 (tm-30)
REVERT: I   80 LYS cc_start: 0.8452 (mttm) cc_final: 0.8245 (mttm)
REVERT: J   45 LYS cc_start: 0.8053 (mtpt) cc_final: 0.7664 (mttt)
REVERT: L   87 SER cc_start: 0.8652 (t) cc_final: 0.8434 (t)
REVERT: M   46 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7788 (tm-30)
REVERT: M   62 GLN cc_start: 0.5026 (pm20) cc_final: 0.4344 (pm20)
REVERT: M   80 LYS cc_start: 0.8418 (mmmt) cc_final: 0.7086 (pttp)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.1889
  time to fit residues: 24.4929
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  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 79 optimal weight:   20.0000
   chunk 68 optimal weight:    9.9990
   chunk 57 optimal weight:   30.0000
   chunk 38 optimal weight:    7.9990
   chunk 53 optimal weight:    6.9990
   chunk 45 optimal weight:   20.0000
   chunk 77 optimal weight:    0.9990
   chunk 74 optimal weight:    4.9990
   chunk 28 optimal weight:   20.0000
   chunk 64 optimal weight:    4.9990
   chunk 9 optimal weight:    0.1980
   overall best weight:    3.6388

-------------------------------------------------------------------------------
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 = 0.4527 r_free = 0.4527 target = 0.174350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.151266 restraints weight = 11621.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.153012 restraints weight = 8819.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.154320 restraints weight = 7315.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.4261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6782
moved from start:          0.7967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5976  Z= 0.191
  Angle     :  0.571   7.433   8052  Z= 0.315
  Chirality :  0.054   0.165   1068
  Planarity :  0.002   0.014    984
  Dihedral  :  4.935  17.086    852
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.11 %
    Favored  : 92.89 %
  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 (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: -2.95 (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
 HIS   0.001   0.000   HIS L  50 
 PHE   0.004   0.001   PHE E  94 
 TYR   0.011   0.002   TYR F  39 

*********************** 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
  95 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.654 
Fit side-chains
REVERT: B   83 GLU cc_start: 0.7226 (tp30) cc_final: 0.6954 (tp30)
REVERT: C   46 GLU cc_start: 0.8565 (tt0) cc_final: 0.8038 (tp30)
REVERT: E   20 GLU cc_start: 0.7434 (mp0) cc_final: 0.7189 (mp0)
REVERT: E   46 GLU cc_start: 0.8357 (tt0) cc_final: 0.7581 (tt0)
REVERT: F   83 GLU cc_start: 0.6347 (tp30) cc_final: 0.5881 (tp30)
REVERT: J   45 LYS cc_start: 0.7991 (mtpt) cc_final: 0.7623 (mttt)
REVERT: K   46 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7643 (tm-30)
REVERT: L   87 SER cc_start: 0.8621 (t) cc_final: 0.8410 (t)
REVERT: M   46 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7823 (tm-30)
REVERT: M   80 LYS cc_start: 0.8297 (mmmt) cc_final: 0.7013 (pttp)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.1783
  time to fit residues: 22.4271
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  : 0.662 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 21 optimal weight:   40.0000
   chunk 63 optimal weight:   30.0000
   chunk 57 optimal weight:   30.0000
   chunk 55 optimal weight:   10.0000
   chunk 61 optimal weight:    9.9990
   chunk 73 optimal weight:   30.0000
   chunk 81 optimal weight:   10.0000
   chunk 11 optimal weight:    7.9990
   chunk 50 optimal weight:    8.9990
   chunk 32 optimal weight:    3.9990
   chunk 64 optimal weight:    6.9990
   overall best weight:    7.5990

-------------------------------------------------------------------------------
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 = 0.4487 r_free = 0.4487 target = 0.168725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.145781 restraints weight = 11996.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.147524 restraints weight = 9284.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.148769 restraints weight = 7749.509|
|-----------------------------------------------------------------------------|
r_work (final): 0.4209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6893
moved from start:          0.8583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   5976  Z= 0.317
  Angle     :  0.697   7.881   8052  Z= 0.381
  Chirality :  0.055   0.157   1068
  Planarity :  0.003   0.015    984
  Dihedral  :  5.907  22.248    852
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 14.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.07 %
    Favored  : 90.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.16 (0.23), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.40 (0.18), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS L  50 
 PHE   0.008   0.002   PHE E  94 
 TYR   0.016   0.002   TYR D  39 

*********************** 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
  91 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.617 
Fit side-chains
REVERT: E   46 GLU cc_start: 0.8380 (tt0) cc_final: 0.7554 (tm-30)
REVERT: F   83 GLU cc_start: 0.6388 (tp30) cc_final: 0.6132 (tp30)
REVERT: K   80 LYS cc_start: 0.8763 (mmtt) cc_final: 0.8311 (mmtt)
REVERT: M   46 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7863 (tm-30)
REVERT: M   80 LYS cc_start: 0.8394 (mmmt) cc_final: 0.7177 (pttp)
  outliers start: 0
  outliers final: 0
  residues processed: 91
  average time/residue: 0.1747
  time to fit residues: 21.0220
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  : 0.613 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 34 optimal weight:   20.0000
   chunk 81 optimal weight:   10.0000
   chunk 35 optimal weight:    5.9990
   chunk 57 optimal weight:   20.0000
   chunk 55 optimal weight:   30.0000
   chunk 59 optimal weight:   20.0000
   chunk 5 optimal weight:    5.9990
   chunk 6 optimal weight:    7.9990
   chunk 48 optimal weight:    6.9990
   chunk 18 optimal weight:   10.0000
   chunk 46 optimal weight:    0.9980
   overall best weight:    5.5988

-------------------------------------------------------------------------------
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 = 0.4512 r_free = 0.4512 target = 0.170352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.147012 restraints weight = 11980.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.149103 restraints weight = 8950.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.150389 restraints weight = 7245.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.4230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6870
moved from start:          0.8609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5976  Z= 0.239
  Angle     :  0.628   6.864   8052  Z= 0.345
  Chirality :  0.054   0.188   1068
  Planarity :  0.002   0.013    984
  Dihedral  :  5.406  19.562    852
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 11.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.48 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  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: -3.15 (0.23), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.39 (0.18), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS I  50 
 PHE   0.006   0.001   PHE E  94 
 TYR   0.013   0.002   TYR F  39 

*********************** 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
  93 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.723 
Fit side-chains
REVERT: B   38 LEU cc_start: 0.8456 (mp) cc_final: 0.8220 (mp)
REVERT: E   20 GLU cc_start: 0.7492 (mp0) cc_final: 0.7226 (mp0)
REVERT: E   46 GLU cc_start: 0.8317 (tt0) cc_final: 0.7579 (tm-30)
REVERT: J   80 LYS cc_start: 0.8214 (mtmm) cc_final: 0.7872 (mtmm)
REVERT: K   80 LYS cc_start: 0.8699 (mmtt) cc_final: 0.8336 (mmtt)
REVERT: M   80 LYS cc_start: 0.8323 (mmmt) cc_final: 0.7054 (pttp)
  outliers start: 0
  outliers final: 0
  residues processed: 93
  average time/residue: 0.1881
  time to fit residues: 22.9159
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  : 0.701 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 62 optimal weight:    6.9990
   chunk 25 optimal weight:    4.9990
   chunk 5 optimal weight:   20.0000
   chunk 55 optimal weight:   20.0000
   chunk 52 optimal weight:    6.9990
   chunk 13 optimal weight:    9.9990
   chunk 41 optimal weight:   20.0000
   chunk 33 optimal weight:    6.9990
   chunk 42 optimal weight:   10.0000
   chunk 80 optimal weight:    4.9990
   chunk 1 optimal weight:   20.0000
   overall best weight:    6.1990

-------------------------------------------------------------------------------
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 = 0.4506 r_free = 0.4506 target = 0.170429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.148319 restraints weight = 11638.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.149996 restraints weight = 8765.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.151296 restraints weight = 7220.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.4242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6895
moved from start:          0.8847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5976  Z= 0.264
  Angle     :  0.651   6.815   8052  Z= 0.358
  Chirality :  0.054   0.171   1068
  Planarity :  0.003   0.027    984
  Dihedral  :  5.527  20.114    852
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.70 %
    Favored  : 91.30 %
  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 (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: -3.24 (0.23), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.46 (0.18), residues: 816

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

********************** 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  : 0.730 
Fit side-chains
   revert: symmetry clash
REVERT: B   38 LEU cc_start: 0.8488 (mp) cc_final: 0.8222 (mp)
REVERT: B   83 GLU cc_start: 0.7265 (tp30) cc_final: 0.7051 (tp30)
REVERT: E   20 GLU cc_start: 0.7501 (mp0) cc_final: 0.7228 (mp0)
REVERT: E   46 GLU cc_start: 0.8378 (tt0) cc_final: 0.7633 (tm-30)
REVERT: F   83 GLU cc_start: 0.6359 (tp30) cc_final: 0.6063 (tp30)
REVERT: K   60 LYS cc_start: 0.6897 (pptt) cc_final: 0.6691 (pptt)
REVERT: K   80 LYS cc_start: 0.8762 (mmtt) cc_final: 0.8342 (mmtt)
REVERT: M   80 LYS cc_start: 0.8379 (mmmt) cc_final: 0.7112 (pttp)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.2580
  time to fit residues: 31.6429
Evaluate side-chains
  71 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 43 optimal weight:   20.0000
   chunk 4 optimal weight:    8.9990
   chunk 40 optimal weight:    7.9990
   chunk 74 optimal weight:    8.9990
   chunk 71 optimal weight:   20.0000
   chunk 53 optimal weight:    9.9990
   chunk 77 optimal weight:    9.9990
   chunk 0 optimal weight:   40.0000
   chunk 20 optimal weight:   20.0000
   chunk 27 optimal weight:   20.0000
   chunk 28 optimal weight:    8.9990
   overall best weight:    8.9990

-------------------------------------------------------------------------------
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**
** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.166525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.144474 restraints weight = 12106.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.146240 restraints weight = 9290.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.147364 restraints weight = 7672.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.4205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6970
moved from start:          0.9250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   5976  Z= 0.351
  Angle     :  0.733   7.279   8052  Z= 0.405
  Chirality :  0.056   0.198   1068
  Planarity :  0.003   0.023    984
  Dihedral  :  6.221  24.017    852
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 14.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.05 %
    Favored  : 89.95 %
  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 (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: -3.50 (0.22), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.66 (0.17), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS L  50 
 PHE   0.009   0.002   PHE E  94 
 TYR   0.018   0.003   TYR D  39 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1780.14 seconds
wall clock time: 32 minutes 34.86 seconds (1954.86 seconds total)