Starting phenix.real_space_refine
on Tue Feb 11 12:56:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cyr_27082/02_2025/8cyr_27082.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cyr_27082/02_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_27082/02_2025/8cyr_27082.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cyr_27082/02_2025/8cyr_27082.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cyr_27082/02_2025/8cyr_27082.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cyr_27082/02_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-5592/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: 1.78, 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: 1.32
  Conformation dependent library (CDL) restraints added in 774.4 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: 1.17
  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: 1.75

  Time building geometry restraints manager: 1.55 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: 0.06
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:             0.060
  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:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.600
  Find NCS groups from input model:        0.140
  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:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.860
-------------------------------------------------------------------------------
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  : 0.610 
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: 0.2384
  time to fit residues: 60.9645
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  : 0.690 
-------------------------------------------------------------------------------
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 = 47)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.148782 restraints weight = 11211.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.150571 restraints weight = 8911.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.151253 restraints weight = 7649.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.4225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6693
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  : 0.607 
Fit side-chains
   revert: symmetry clash
REVERT: C   46 GLU cc_start: 0.8487 (tt0) cc_final: 0.7979 (tt0)
REVERT: E   46 GLU cc_start: 0.8442 (tt0) cc_final: 0.7467 (tm-30)
REVERT: J   45 LYS cc_start: 0.7998 (mtpt) cc_final: 0.7630 (mtpp)
REVERT: J   83 GLU cc_start: 0.7108 (tt0) cc_final: 0.6639 (tt0)
REVERT: J   92 THR cc_start: 0.7635 (p) cc_final: 0.7413 (p)
REVERT: M   43 LYS cc_start: 0.7026 (mmpt) cc_final: 0.6813 (mmmt)
REVERT: M   80 LYS cc_start: 0.8106 (mmmt) cc_final: 0.6674 (pttp)
  outliers start: 2
  outliers final: 0
  residues processed: 110
  average time/residue: 0.2323
  time to fit residues: 31.8412
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  : 0.637 
-------------------------------------------------------------------------------
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:    0.0070
   chunk 34 optimal weight:    6.9990
   chunk 73 optimal weight:    1.9990
   chunk 31 optimal weight:   10.0000
   chunk 77 optimal weight:   20.0000
   chunk 74 optimal weight:    0.5980
   chunk 69 optimal weight:   20.0000
   overall best weight:    1.6602

-------------------------------------------------------------------------------
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 = 0.4592 r_free = 0.4592 target = 0.183544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.156085 restraints weight = 11119.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.158029 restraints weight = 8647.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.159412 restraints weight = 7194.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.4319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6597
moved from start:          0.5826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   5976  Z= 0.157
  Angle     :  0.502   9.673   8052  Z= 0.282
  Chirality :  0.053   0.164   1068
  Planarity :  0.002   0.011    984
  Dihedral  :  4.316  14.192    852
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  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: -2.33 (0.27), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.76 (0.21), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS I  50 
 PHE   0.006   0.001   PHE D  94 
 TYR   0.007   0.001   TYR F  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
  105 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.664 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   83 GLU cc_start: 0.7219 (tp30) cc_final: 0.6991 (tp30)
REVERT: C   80 LYS cc_start: 0.4874 (mmpt) cc_final: 0.4434 (mmmt)
REVERT: E   46 GLU cc_start: 0.8511 (tt0) cc_final: 0.7575 (tm-30)
REVERT: J   45 LYS cc_start: 0.7665 (mtpt) cc_final: 0.7318 (mttt)
REVERT: J   92 THR cc_start: 0.7313 (p) cc_final: 0.6947 (m)
REVERT: M   59 THR cc_start: 0.3871 (p) cc_final: 0.3632 (p)
REVERT: M   80 LYS cc_start: 0.7967 (mmmt) cc_final: 0.6511 (pttp)
REVERT: N   44 THR cc_start: 0.6868 (p) cc_final: 0.6601 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.2152
  time to fit residues: 28.6927
Evaluate side-chains
  66 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 46 optimal weight:    8.9990
   chunk 50 optimal weight:    0.1980
   chunk 43 optimal weight:   30.0000
   chunk 44 optimal weight:    5.9990
   chunk 52 optimal weight:    6.9990
   chunk 41 optimal weight:   20.0000
   chunk 24 optimal weight:   10.0000
   chunk 57 optimal weight:    6.9990
   overall best weight:    5.8388

-------------------------------------------------------------------------------
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**
** 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 = 0.4529 r_free = 0.4529 target = 0.174839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.148838 restraints weight = 11408.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.150825 restraints weight = 8770.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.152082 restraints weight = 7224.485|
|-----------------------------------------------------------------------------|
r_work (final): 0.4250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6718
moved from start:          0.6750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   5976  Z= 0.279
  Angle     :  0.609   9.268   8052  Z= 0.339
  Chirality :  0.052   0.177   1068
  Planarity :  0.003   0.020    984
  Dihedral  :  5.103  20.318    852
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  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: -2.65 (0.26), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.01 (0.20), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS L  50 
 PHE   0.010   0.002   PHE A  94 
 TYR   0.015   0.002   TYR L  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
  98 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.606 
Fit side-chains
   revert: symmetry clash
REVERT: C   46 GLU cc_start: 0.8622 (tt0) cc_final: 0.7782 (tp30)
REVERT: E   46 GLU cc_start: 0.8360 (tt0) cc_final: 0.7687 (tt0)
REVERT: F   83 GLU cc_start: 0.6137 (tp30) cc_final: 0.5822 (tp30)
REVERT: M   80 LYS cc_start: 0.8342 (mmmt) cc_final: 0.6883 (pttp)
REVERT: N   44 THR cc_start: 0.7185 (p) cc_final: 0.6832 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.1914
  time to fit residues: 24.3930
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  : 0.701 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 1 optimal weight:   20.0000
   chunk 6 optimal weight:   20.0000
   chunk 10 optimal weight:    8.9990
   chunk 73 optimal weight:   20.0000
   chunk 12 optimal weight:   20.0000
   chunk 25 optimal weight:    5.9990
   chunk 82 optimal weight:   20.0000
   chunk 42 optimal weight:   30.0000
   chunk 33 optimal weight:   20.0000
   overall best weight:   14.9996

-------------------------------------------------------------------------------
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 = 0.4391 r_free = 0.4391 target = 0.159495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.137061 restraints weight = 12027.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.138552 restraints weight = 9336.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.139668 restraints weight = 7857.744|
|-----------------------------------------------------------------------------|
r_work (final): 0.4110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6990
moved from start:          0.8570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.078   5976  Z= 0.586
  Angle     :  0.972  11.471   8052  Z= 0.536
  Chirality :  0.061   0.215   1068
  Planarity :  0.005   0.022    984
  Dihedral  :  7.761  34.347    852
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 21.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.03 %
    Favored  : 88.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.36 %

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: -3.68 (0.22), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.79 (0.17), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS L  50 
 PHE   0.014   0.003   PHE A  94 
 TYR   0.021   0.004   TYR L  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
  108 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.629 
Fit side-chains
   revert: symmetry clash
REVERT: B   61 GLU cc_start: 0.4629 (pt0) cc_final: 0.4318 (pt0)
REVERT: C   46 GLU cc_start: 0.8423 (tt0) cc_final: 0.7836 (tt0)
REVERT: E   20 GLU cc_start: 0.7392 (mp0) cc_final: 0.7011 (mp0)
REVERT: E   46 GLU cc_start: 0.8224 (tt0) cc_final: 0.7902 (tt0)
REVERT: L   61 GLU cc_start: 0.4500 (pt0) cc_final: 0.3982 (pt0)
REVERT: M   46 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7933 (tm-30)
REVERT: M   80 LYS cc_start: 0.8608 (mmmt) cc_final: 0.7498 (pttp)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.1752
  time to fit residues: 24.7830
Evaluate side-chains
  83 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
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:   30.0000
   chunk 47 optimal weight:    7.9990
   chunk 48 optimal weight:   20.0000
   chunk 76 optimal weight:   30.0000
   chunk 2 optimal weight:    6.9990
   chunk 12 optimal weight:    4.9990
   chunk 44 optimal weight:    8.9990
   chunk 70 optimal weight:    6.9990
   chunk 24 optimal weight:   10.0000
   chunk 61 optimal weight:    4.9990
   chunk 40 optimal weight:    6.9990
   overall best weight:    6.1990

-------------------------------------------------------------------------------
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**
** C  62 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 = 0.4482 r_free = 0.4482 target = 0.168408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.145150 restraints weight = 11936.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.146867 restraints weight = 9284.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.147948 restraints weight = 7790.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.4199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6918
moved from start:          0.8450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   5976  Z= 0.270
  Angle     :  0.668   9.760   8052  Z= 0.368
  Chirality :  0.055   0.166   1068
  Planarity :  0.003   0.019    984
  Dihedral  :  5.932  22.338    852
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.60 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  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: -3.47 (0.22), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.64 (0.17), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B  50 
 PHE   0.004   0.001   PHE L  94 
 TYR   0.013   0.002   TYR D  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
  109 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.631 
Fit side-chains
REVERT: B   61 GLU cc_start: 0.4657 (pt0) cc_final: 0.4370 (pt0)
REVERT: E   43 LYS cc_start: 0.8845 (mppt) cc_final: 0.8606 (mttt)
REVERT: F   83 GLU cc_start: 0.6323 (tp30) cc_final: 0.5763 (tp30)
REVERT: L   44 THR cc_start: 0.7897 (t) cc_final: 0.7543 (m)
REVERT: L   45 LYS cc_start: 0.8062 (mtpt) cc_final: 0.7437 (mttp)
REVERT: M   46 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7879 (tm-30)
REVERT: M   80 LYS cc_start: 0.8480 (mmmt) cc_final: 0.7373 (pttp)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.1786
  time to fit residues: 25.6271
Evaluate side-chains
  81 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
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:    0.0060
   chunk 68 optimal weight:    9.9990
   chunk 57 optimal weight:   40.0000
   chunk 38 optimal weight:   20.0000
   chunk 53 optimal weight:    6.9990
   chunk 45 optimal weight:    7.9990
   chunk 77 optimal weight:    9.9990
   chunk 74 optimal weight:    4.9990
   chunk 28 optimal weight:   40.0000
   chunk 64 optimal weight:   30.0000
   chunk 9 optimal weight:    8.9990
   overall best weight:    5.8004

-------------------------------------------------------------------------------
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 ** 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 = 0.4498 r_free = 0.4498 target = 0.169236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.145701 restraints weight = 11819.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.147401 restraints weight = 9124.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.148639 restraints weight = 7639.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.4214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6923
moved from start:          0.8615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5976  Z= 0.258
  Angle     :  0.658   8.493   8052  Z= 0.361
  Chirality :  0.055   0.166   1068
  Planarity :  0.002   0.014    984
  Dihedral  :  5.622  21.168    852
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 13.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  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 (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: -3.38 (0.23), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.57 (0.17), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS L  50 
 PHE   0.005   0.001   PHE E  94 
 TYR   0.015   0.002   TYR D  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
  102 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.661 
Fit side-chains
REVERT: D   83 GLU cc_start: 0.6003 (tp30) cc_final: 0.5779 (tp30)
REVERT: F   83 GLU cc_start: 0.6307 (tp30) cc_final: 0.5886 (tp30)
REVERT: J   38 LEU cc_start: 0.8351 (mt) cc_final: 0.8087 (mt)
REVERT: L   44 THR cc_start: 0.7726 (t) cc_final: 0.7402 (m)
REVERT: L   45 LYS cc_start: 0.8054 (mtpt) cc_final: 0.7290 (mttp)
REVERT: M   46 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7846 (tm-30)
REVERT: M   80 LYS cc_start: 0.8477 (mmmt) cc_final: 0.7326 (pttp)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.1859
  time to fit residues: 25.0092
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  : 0.637 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 57 optimal weight:   30.0000
   chunk 55 optimal weight:   30.0000
   chunk 61 optimal weight:    7.9990
   chunk 73 optimal weight:    0.5980
   chunk 81 optimal weight:   20.0000
   chunk 11 optimal weight:    0.9980
   chunk 50 optimal weight:   20.0000
   chunk 32 optimal weight:    3.9990
   chunk 64 optimal weight:   20.0000
   overall best weight:    6.7188

-------------------------------------------------------------------------------
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  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 = 0.4496 r_free = 0.4496 target = 0.168549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.145456 restraints weight = 11919.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.147192 restraints weight = 9193.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.148411 restraints weight = 7657.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.4212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6929
moved from start:          0.8857

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= 0.281
  Angle     :  0.676   8.209   8052  Z= 0.371
  Chirality :  0.055   0.177   1068
  Planarity :  0.002   0.015    984
  Dihedral  :  5.717  21.548    852
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 13.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.58 %
    Favored  : 91.42 %
  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: -3.40 (0.23), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.59 (0.17), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS L  50 
 PHE   0.006   0.001   PHE E  94 
 TYR   0.015   0.002   TYR B  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
  103 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.656 
Fit side-chains
REVERT: D   83 GLU cc_start: 0.6081 (tp30) cc_final: 0.5794 (tp30)
REVERT: F   83 GLU cc_start: 0.6293 (tp30) cc_final: 0.5784 (tp30)
REVERT: J   80 LYS cc_start: 0.7846 (ptpt) cc_final: 0.7510 (ptpt)
REVERT: K   60 LYS cc_start: 0.6835 (pttt) cc_final: 0.6523 (pptt)
REVERT: L   44 THR cc_start: 0.7803 (t) cc_final: 0.7450 (m)
REVERT: L   45 LYS cc_start: 0.7916 (mtpt) cc_final: 0.7234 (mttp)
REVERT: M   80 LYS cc_start: 0.8472 (mmmt) cc_final: 0.7307 (pttp)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.1882
  time to fit residues: 25.2759
Evaluate side-chains
  80 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
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:   30.0000
   chunk 81 optimal weight:    6.9990
   chunk 35 optimal weight:    8.9990
   chunk 57 optimal weight:   30.0000
   chunk 55 optimal weight:    9.9990
   chunk 59 optimal weight:    6.9990
   chunk 5 optimal weight:    9.9990
   chunk 6 optimal weight:    5.9990
   chunk 48 optimal weight:    8.9990
   chunk 18 optimal weight:   10.0000
   chunk 46 optimal weight:    3.9990
   overall best weight:    6.5990

-------------------------------------------------------------------------------
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**
** 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 = 0.4503 r_free = 0.4503 target = 0.168990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.146438 restraints weight = 11918.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.148225 restraints weight = 9061.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.149453 restraints weight = 7480.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.4219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6935
moved from start:          0.9076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5976  Z= 0.277
  Angle     :  0.686   7.739   8052  Z= 0.376
  Chirality :  0.055   0.171   1068
  Planarity :  0.003   0.021    984
  Dihedral  :  5.690  21.164    852
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 13.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.82 %
    Favored  : 91.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  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: -3.47 (0.22), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.64 (0.17), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS L  50 
 PHE   0.006   0.001   PHE E  94 
 TYR   0.016   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
  98 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.617 
Fit side-chains
REVERT: D   83 GLU cc_start: 0.5986 (tp30) cc_final: 0.5687 (tp30)
REVERT: F   39 TYR cc_start: 0.7681 (t80) cc_final: 0.7467 (t80)
REVERT: F   83 GLU cc_start: 0.6227 (tp30) cc_final: 0.5781 (tp30)
REVERT: L   44 THR cc_start: 0.7750 (t) cc_final: 0.7405 (m)
REVERT: L   45 LYS cc_start: 0.7894 (mtpt) cc_final: 0.7216 (mttp)
REVERT: M   80 LYS cc_start: 0.8469 (mmmt) cc_final: 0.7278 (pttp)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.1621
  time to fit residues: 21.6216
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  : 0.684 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 25 optimal weight:    0.9990
   chunk 5 optimal weight:    9.9990
   chunk 55 optimal weight:   30.0000
   chunk 52 optimal weight:    7.9990
   chunk 13 optimal weight:    9.9990
   chunk 41 optimal weight:   20.0000
   chunk 33 optimal weight:    2.9990
   chunk 42 optimal weight:    7.9990
   chunk 80 optimal weight:    5.9990
   chunk 1 optimal weight:   20.0000
   overall best weight:    5.1990

-------------------------------------------------------------------------------
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  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 = 0.4524 r_free = 0.4524 target = 0.170344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.147387 restraints weight = 11838.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.149076 restraints weight = 9157.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.150393 restraints weight = 7660.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.4236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6908
moved from start:          0.9157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5976  Z= 0.240
  Angle     :  0.644   7.995   8052  Z= 0.353
  Chirality :  0.055   0.167   1068
  Planarity :  0.002   0.021    984
  Dihedral  :  5.372  18.718    852
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 13.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.60 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -3.42 (0.22), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.60 (0.17), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS I  50 
 PHE   0.007   0.001   PHE A  94 
 TYR   0.014   0.002   TYR J  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
  103 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.619 
Fit side-chains
REVERT: E   46 GLU cc_start: 0.8220 (tt0) cc_final: 0.7735 (tm-30)
REVERT: F   83 GLU cc_start: 0.6256 (tp30) cc_final: 0.5978 (tp30)
REVERT: K   62 GLN cc_start: 0.6378 (mp-120) cc_final: 0.6071 (mp10)
REVERT: L   44 THR cc_start: 0.7696 (t) cc_final: 0.7326 (m)
REVERT: L   45 LYS cc_start: 0.7842 (mtpt) cc_final: 0.7234 (mttp)
REVERT: M   80 LYS cc_start: 0.8460 (mmmt) cc_final: 0.7240 (pttp)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.1725
  time to fit residues: 23.3779
Evaluate side-chains
  79 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
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:   40.0000
   chunk 4 optimal weight:    4.9990
   chunk 40 optimal weight:   20.0000
   chunk 74 optimal weight:    0.6980
   chunk 71 optimal weight:    2.9990
   chunk 53 optimal weight:    7.9990
   chunk 77 optimal weight:   20.0000
   chunk 0 optimal weight:   40.0000
   chunk 20 optimal weight:    8.9990
   chunk 27 optimal weight:   30.0000
   chunk 28 optimal weight:   20.0000
   overall best weight:    5.1388

-------------------------------------------------------------------------------
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  62 GLN
** 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 = 0.4532 r_free = 0.4532 target = 0.170014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.147868 restraints weight = 11791.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.149622 restraints weight = 8891.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.150897 restraints weight = 7293.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.4253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6911
moved from start:          0.9311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5976  Z= 0.233
  Angle     :  0.626   6.632   8052  Z= 0.346
  Chirality :  0.054   0.169   1068
  Planarity :  0.002   0.023    984
  Dihedral  :  5.319  18.697    852
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.23 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.39 (0.23), residues: 816
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.58 (0.17), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS L  50 
 PHE   0.004   0.001   PHE E  94 
 TYR   0.018   0.002   TYR F  39 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1643.05 seconds
wall clock time: 30 minutes 36.34 seconds (1836.34 seconds total)