Starting phenix.real_space_refine
on Thu Feb  5 12:47:18 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9w74_65716/02_2026/9w74_65716.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9w74_65716/02_2026/9w74_65716.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.94
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9w74_65716/02_2026/9w74_65716.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9w74_65716/02_2026/9w74_65716.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9w74_65716/02_2026/9w74_65716.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9w74_65716/02_2026/9w74_65716.cif"
  }
  resolution = 4.94
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.043
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: 5
    Type Number    sf(0)   Gaussians
     P     412      5.49       5
     S      20      5.16       5
     C    9679      2.51       5
     N    3130      2.21       5
     O    4022      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 17263
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "A"
      Number of atoms: 740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 740
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 2, 'TRANS': 87}
    Chain: "B"
      Number of atoms: 661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 661
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 795
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 795
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 5, 'TRANS': 97}
    Chain: "D"
      Number of atoms: 745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 745
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 801
          Classifications: {'peptide': 97}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 618
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "K"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 802
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "L"
      Number of atoms: 661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 661
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "M"
      Number of atoms: 795
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 795
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 5, 'TRANS': 97}
    Chain: "N"
      Number of atoms: 745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 745
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "O"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 801
          Classifications: {'peptide': 97}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "P"
      Number of atoms: 618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 618
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "I"
      Number of atoms: 4344
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 207, 4344
          Classifications: {'DNA': 207}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 206}
    Chain: "J"
      Number of atoms: 4137
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 207, 4137
          Classifications: {'DNA': 207}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 206}
  Time building chain proxies: 3.78, per 1000 atoms: 0.22
  Number of scatterers: 17263
  At special positions: 0
  Unit cell: (103.88, 119.78, 150.52, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      20     16.00
     P     412     15.00
     O    4022      8.00
     N    3130      7.00
     C    9679      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: 1.59
  Conformation dependent library (CDL) restraints added in 451.0 milliseconds
  

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2060

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 8 sheets defined
      73.6% alpha, 1.5% beta
      201 base pairs and 382 stacking pairs defined.
    Time for finding SS restraints: 2.90
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 57
      removed outlier: 4.253A  pdb=" N   SER A  57 " --> pdb=" O   ARG A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 77
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.706A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.701A  pdb=" N   ILE B  29 " --> pdb=" O   ASN B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 50 through 77
    Processing helix  chain 'B' and resid 82 through 94
    Processing helix  chain 'C' and resid 17 through 22
    Processing helix  chain 'C' and resid 26 through 38
      removed outlier: 3.718A  pdb=" N   ASN C  38 " --> pdb=" O   LEU C  34 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.463A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.670A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
      removed outlier: 3.685A  pdb=" N   LEU C 116 " --> pdb=" O   SER C 113 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 100 through 121
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 76
      removed outlier: 4.278A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   GLN E  76 " --> pdb=" O   ARG E  72 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.920A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
      removed outlier: 3.770A  pdb=" N   ILE F  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 47 through 76
      removed outlier: 4.228A  pdb=" N   TYR F  51 " --> pdb=" O   SER F  47 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   GLU F  52 " --> pdb=" O   GLY F  48 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 92
    Processing helix  chain 'K' and resid 44 through 56
    Processing helix  chain 'K' and resid 63 through 79
    Processing helix  chain 'K' and resid 85 through 114
    Processing helix  chain 'K' and resid 120 through 132
      removed outlier: 3.539A  pdb=" N   ILE K 124 " --> pdb=" O   MET K 120 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 24 through 29
      removed outlier: 3.884A  pdb=" N   GLN L  27 " --> pdb=" O   ASP L  24 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ILE L  29 " --> pdb=" O   ILE L  26 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 30 through 41
    Processing helix  chain 'L' and resid 49 through 76
      removed outlier: 3.822A  pdb=" N   GLU L  53 " --> pdb=" O   LEU L  49 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 82 through 93
    Processing helix  chain 'M' and resid 17 through 22
    Processing helix  chain 'M' and resid 26 through 37
    Processing helix  chain 'M' and resid 45 through 73
      removed outlier: 4.226A  pdb=" N   VAL M  49 " --> pdb=" O   ALA M  45 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 79 through 90
    Processing helix  chain 'M' and resid 90 through 97
    Processing helix  chain 'N' and resid 34 through 46
    Processing helix  chain 'N' and resid 52 through 81
    Processing helix  chain 'N' and resid 87 through 99
      removed outlier: 3.603A  pdb=" N   ILE N  91 " --> pdb=" O   THR N  87 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 100 through 121
    Processing helix  chain 'O' and resid 44 through 57
    Processing helix  chain 'O' and resid 63 through 76
      removed outlier: 3.617A  pdb=" N   PHE O  67 " --> pdb=" O   ARG O  63 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 85 through 114
    Processing helix  chain 'O' and resid 121 through 132
    Processing helix  chain 'P' and resid 30 through 41
    Processing helix  chain 'P' and resid 47 through 75
      removed outlier: 3.924A  pdb=" N   TYR P  51 " --> pdb=" O   SER P  47 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   GLU P  52 " --> pdb=" O   GLY P  48 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 82 through 93
    Processing sheet with id=AA1, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.553A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'C' and resid 100 through 101
    Processing sheet with id=AA3, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA4, first strand: chain 'K' and resid 83 through 84
    Processing sheet with id=AA5, first strand: chain 'K' and resid 118 through 119
      removed outlier: 7.089A  pdb=" N   ARG L  45 " --> pdb=" O   ILE K 119 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'M' and resid 42 through 43
      removed outlier: 7.924A  pdb=" N   ARG M  42 " --> pdb=" O   ILE N  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'M' and resid 100 through 101
    Processing sheet with id=AA8, first strand: chain 'O' and resid 118 through 119

    594 hydrogen bonds defined for protein.
    1773 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      402 hydrogen bonds
      804 hydrogen bond angles
      0 basepair planarities
      201 basepair parallelities
      382 stacking parallelities
  Total time for adding SS restraints: 4.28

  Time building geometry restraints manager: 2.13 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2790
        1.33 -     1.45: 6256
        1.45 -     1.57: 8502
        1.57 -     1.69: 824
        1.69 -     1.81: 36
  Bond restraints: 18408
  Sorted by residual:
  bond pdb=" CG  GLU D 110 "
       pdb=" CD  GLU D 110 "
    ideal  model  delta    sigma   weight residual
    1.516  1.478  0.038 2.50e-02 1.60e+03 2.33e+00
  bond pdb=" C3'  DA I 102 "
       pdb=" O3'  DA I 102 "
    ideal  model  delta    sigma   weight residual
    1.422  1.466 -0.044 3.00e-02 1.11e+03 2.17e+00
  bond pdb=" C1'  DT J -96 "
       pdb=" N1   DT J -96 "
    ideal  model  delta    sigma   weight residual
    1.490  1.450  0.040 3.00e-02 1.11e+03 1.75e+00
  bond pdb=" CD  GLU D 110 "
       pdb=" OE1 GLU D 110 "
    ideal  model  delta    sigma   weight residual
    1.249  1.225  0.024 1.90e-02 2.77e+03 1.61e+00
  bond pdb=" CG  ARG K  52 "
       pdb=" CD  ARG K  52 "
    ideal  model  delta    sigma   weight residual
    1.520  1.483  0.037 3.00e-02 1.11e+03 1.53e+00
  ... (remaining 18403 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.68: 25244
        1.68 -     3.35: 1274
        3.35 -     5.03: 85
        5.03 -     6.70: 22
        6.70 -     8.38: 3
  Bond angle restraints: 26628
  Sorted by residual:
  angle pdb=" C   GLU A 105 "
        pdb=" N   ASP A 106 "
        pdb=" CA  ASP A 106 "
      ideal   model   delta    sigma   weight residual
     120.31  113.62    6.69 1.52e+00 4.33e-01 1.94e+01
  angle pdb=" N   GLU K 105 "
        pdb=" CA  GLU K 105 "
        pdb=" CB  GLU K 105 "
      ideal   model   delta    sigma   weight residual
     110.16  116.16   -6.00 1.48e+00 4.57e-01 1.64e+01
  angle pdb=" N   GLU D 110 "
        pdb=" CA  GLU D 110 "
        pdb=" CB  GLU D 110 "
      ideal   model   delta    sigma   weight residual
     110.28  116.29   -6.01 1.55e+00 4.16e-01 1.50e+01
  angle pdb=" N   GLU M  56 "
        pdb=" CA  GLU M  56 "
        pdb=" CB  GLU M  56 "
      ideal   model   delta    sigma   weight residual
     110.12  115.76   -5.64 1.47e+00 4.63e-01 1.47e+01
  angle pdb=" N   GLU K  94 "
        pdb=" CA  GLU K  94 "
        pdb=" CB  GLU K  94 "
      ideal   model   delta    sigma   weight residual
     110.28  115.47   -5.19 1.55e+00 4.16e-01 1.12e+01
  ... (remaining 26623 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.59: 8166
       34.59 -    69.18: 2211
       69.18 -   103.76: 102
      103.76 -   138.35: 1
      138.35 -   172.94: 2
  Dihedral angle restraints: 10482
    sinusoidal: 7292
      harmonic: 3190
  Sorted by residual:
  dihedral pdb=" CA  GLN P  27 "
           pdb=" C   GLN P  27 "
           pdb=" N   GLY P  28 "
           pdb=" CA  GLY P  28 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.36   22.64     0      5.00e+00 4.00e-02 2.05e+01
  dihedral pdb=" CA  LYS E  64 "
           pdb=" C   LYS E  64 "
           pdb=" N   LEU E  65 "
           pdb=" CA  LEU E  65 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.05  -20.95     0      5.00e+00 4.00e-02 1.76e+01
  dihedral pdb=" CA  ARG B  23 "
           pdb=" C   ARG B  23 "
           pdb=" N   ASP B  24 "
           pdb=" CA  ASP B  24 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.34   20.66     0      5.00e+00 4.00e-02 1.71e+01
  ... (remaining 10479 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 2183
       0.040 -    0.080: 699
       0.080 -    0.121: 124
       0.121 -    0.161: 23
       0.161 -    0.201: 3
  Chirality restraints: 3032
  Sorted by residual:
  chirality pdb=" CB  ILE E 130 "
            pdb=" CA  ILE E 130 "
            pdb=" CG1 ILE E 130 "
            pdb=" CG2 ILE E 130 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" CA  GLU A 105 "
            pdb=" N   GLU A 105 "
            pdb=" C   GLU A 105 "
            pdb=" CB  GLU A 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.86e-01
  chirality pdb=" CB  VAL A 101 "
            pdb=" CA  VAL A 101 "
            pdb=" CG1 VAL A 101 "
            pdb=" CG2 VAL A 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 7.10e-01
  ... (remaining 3029 not shown)

  Planarity restraints: 1934
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE M  79 "   -0.044 5.00e-02 4.00e+02   6.74e-02 7.27e+00
        pdb=" N   PRO M  80 "    0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO M  80 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO M  80 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE K 104 "   -0.014 2.00e-02 2.50e+03   1.82e-02 5.82e+00
        pdb=" CG  PHE K 104 "    0.042 2.00e-02 2.50e+03
        pdb=" CD1 PHE K 104 "   -0.016 2.00e-02 2.50e+03
        pdb=" CD2 PHE K 104 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE1 PHE K 104 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE K 104 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE K 104 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A  93 "    0.011 2.00e-02 2.50e+03   2.12e-02 4.48e+00
        pdb=" C   GLN A  93 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   GLN A  93 "    0.014 2.00e-02 2.50e+03
        pdb=" N   GLU A  94 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1931 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.83: 4976
        2.83 -     3.35: 19590
        3.35 -     3.87: 37317
        3.87 -     4.38: 41860
        4.38 -     4.90: 55004
  Nonbonded interactions: 158747
  Sorted by model distance:
  nonbonded pdb=" O   HIS D 106 "
            pdb=" OE1 GLU D 110 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" O   VAL A 101 "
            pdb=" OE1 GLU A 105 "
     model   vdw
     2.367 3.040
  nonbonded pdb=" O   GLN A  93 "
            pdb=" OE1 GLU A  97 "
     model   vdw
     2.370 3.040
  nonbonded pdb=" O   MET K  90 "
            pdb=" OE1 GLU K  94 "
     model   vdw
     2.373 3.040
  nonbonded pdb=" O   VAL K 101 "
            pdb=" OE1 GLU K 105 "
     model   vdw
     2.386 3.040
  ... (remaining 158742 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'E' and resid 45 through 134)
  selection = (chain 'K' and resid 45 through 134)
  selection = (chain 'O' and resid 45 through 134)
}
ncs_group {
  reference = (chain 'B' and resid 25 through 102)
  selection = chain 'F'
  selection = (chain 'L' and resid 25 through 102)
  selection = chain 'P'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'M'
}
ncs_group {
  reference = chain 'D'
  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:             1.660
  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:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     19.530
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
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      :  0.006   0.044  18408  Z= 0.268
  Angle     :  0.770   8.380  26628  Z= 0.460
  Chirality :  0.040   0.201   3032
  Planarity :  0.006   0.067   1934
  Dihedral  : 29.700 172.938   8422
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 27.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.24), residues: 1075
  helix:  0.51 (0.18), residues: 773
  sheet:  None (None), residues: 0
  loop : -1.40 (0.34), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG K  83 
 TYR   0.022   0.002   TYR A  54 
 PHE   0.042   0.003   PHE K 104 
 HIS   0.008   0.002   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00564 (18408)
  covalent geometry    : angle       0.77009 (26628)
  hydrogen bonds       : bond        0.12102 (  996)
  hydrogen bonds       : angle       5.48595 ( 2577)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.459 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.9334 (tpt) cc_final: 0.9093 (mmm)
REVERT: A  130 ILE cc_start: 0.9515 (mp) cc_final: 0.8525 (mp)
REVERT: D   65 ASP cc_start: 0.9757 (t0) cc_final: 0.9420 (t0)
REVERT: D   69 ARG cc_start: 0.9196 (mtp180) cc_final: 0.8778 (ptp-170)
REVERT: E   67 PHE cc_start: 0.8809 (t80) cc_final: 0.8405 (t80)
REVERT: E  106 ASP cc_start: 0.9304 (m-30) cc_final: 0.9075 (m-30)
REVERT: E  129 ARG cc_start: 0.9721 (tpp-160) cc_final: 0.9417 (tmm160)
REVERT: F   44 LYS cc_start: 0.9476 (mtmt) cc_final: 0.9271 (tmtt)
REVERT: F   61 PHE cc_start: 0.9156 (t80) cc_final: 0.8913 (t80)
REVERT: K   55 GLN cc_start: 0.7702 (tp40) cc_final: 0.7236 (mm110)
REVERT: K  108 ASN cc_start: 0.8222 (t0) cc_final: 0.7988 (m-40)
REVERT: M   95 LYS cc_start: 0.9500 (tppt) cc_final: 0.9247 (tmmt)
REVERT: N   56 MET cc_start: 0.9520 (ptp) cc_final: 0.9275 (mpp)
REVERT: N  110 GLU cc_start: 0.9384 (mm-30) cc_final: 0.8948 (tp30)
REVERT: O   93 GLN cc_start: 0.9736 (tp-100) cc_final: 0.9132 (tp-100)
REVERT: O   97 GLU cc_start: 0.9774 (mt-10) cc_final: 0.9256 (mt-10)
REVERT: P   59 LYS cc_start: 0.8837 (mttp) cc_final: 0.8478 (mmmt)
REVERT: P   88 TYR cc_start: 0.9667 (t80) cc_final: 0.9219 (t80)
REVERT: P   95 ARG cc_start: 0.9491 (mmp80) cc_final: 0.9291 (mmm160)
  outliers start: 0
  outliers final: 0
  residues processed: 184
  average time/residue: 0.1465
  time to fit residues: 40.1008
Evaluate side-chains
  129 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 98 optimal weight:   40.0000
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:   20.0000
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:   10.0000
   chunk 103 optimal weight:    8.9990
   chunk 77 optimal weight:    7.9990
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:   10.0000
   chunk 55 optimal weight:    7.9990
   overall best weight:    7.5992

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 110 ASN
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 104 GLN
** N  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 106 HIS
O 108 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.044072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.032245 restraints weight = 250207.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.033246 restraints weight = 152847.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.033966 restraints weight = 107376.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.034485 restraints weight = 82384.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.034860 restraints weight = 67125.077|
|-----------------------------------------------------------------------------|
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.1494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.092  18408  Z= 0.335
  Angle     :  0.791  10.380  26628  Z= 0.473
  Chirality :  0.042   0.191   3032
  Planarity :  0.006   0.060   1934
  Dihedral  : 33.495 168.727   6222
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 36.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  8.91 %
    Favored  : 90.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.33 (0.24), residues: 1075
  helix:  0.36 (0.18), residues: 777
  sheet:  None (None), residues: 0
  loop : -1.59 (0.34), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG K  52 
 TYR   0.025   0.002   TYR C  39 
 PHE   0.031   0.003   PHE K 104 
 HIS   0.009   0.002   HIS N  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00708 (18408)
  covalent geometry    : angle       0.79087 (26628)
  hydrogen bonds       : bond        0.13704 (  996)
  hydrogen bonds       : angle       5.31968 ( 2577)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 170
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 GLU cc_start: 0.9558 (mp0) cc_final: 0.9319 (mp0)
REVERT: A  130 ILE cc_start: 0.9803 (OUTLIER) cc_final: 0.9411 (tp)
REVERT: C   64 GLU cc_start: 0.9237 (tp30) cc_final: 0.8828 (tp30)
REVERT: E   67 PHE cc_start: 0.8850 (t80) cc_final: 0.8403 (t80)
REVERT: E  129 ARG cc_start: 0.9746 (tpp-160) cc_final: 0.9484 (tmm160)
REVERT: F   44 LYS cc_start: 0.9506 (mtmt) cc_final: 0.9284 (tmtt)
REVERT: K   55 GLN cc_start: 0.7729 (tp40) cc_final: 0.7294 (mm110)
REVERT: K  108 ASN cc_start: 0.8175 (t0) cc_final: 0.7943 (m-40)
REVERT: M  104 GLN cc_start: 0.7231 (OUTLIER) cc_final: 0.6755 (pp30)
REVERT: N  110 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8816 (tp30)
REVERT: O   93 GLN cc_start: 0.9756 (tp-100) cc_final: 0.9292 (tm-30)
REVERT: P   59 LYS cc_start: 0.8817 (mttp) cc_final: 0.8440 (mmmt)
REVERT: P   88 TYR cc_start: 0.9608 (t80) cc_final: 0.9203 (t80)
  outliers start: 7
  outliers final: 3
  residues processed: 176
  average time/residue: 0.1329
  time to fit residues: 35.6103
Evaluate side-chains
  125 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 120
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 71 optimal weight:    6.9990
   chunk 125 optimal weight:   10.0000
   chunk 112 optimal weight:   10.0000
   chunk 43 optimal weight:    3.9990
   chunk 63 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 127 optimal weight:   10.0000
   chunk 12 optimal weight:    6.9990
   chunk 87 optimal weight:    7.9990
   chunk 113 optimal weight:    7.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 106 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.046119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.034353 restraints weight = 249104.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.035416 restraints weight = 148969.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.036167 restraints weight = 102503.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.036719 restraints weight = 77905.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.037106 restraints weight = 63014.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.1722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  18408  Z= 0.233
  Angle     :  0.722   7.618  26628  Z= 0.433
  Chirality :  0.039   0.153   3032
  Planarity :  0.005   0.062   1934
  Dihedral  : 33.355 161.956   6222
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 25.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  6.30 %
    Favored  : 93.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.09 (0.24), residues: 1075
  helix:  0.68 (0.18), residues: 772
  sheet:  None (None), residues: 0
  loop : -1.41 (0.34), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG E 134 
 TYR   0.019   0.002   TYR P  72 
 PHE   0.031   0.002   PHE K 104 
 HIS   0.006   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 (18408)
  covalent geometry    : angle       0.72173 (26628)
  hydrogen bonds       : bond        0.09351 (  996)
  hydrogen bonds       : angle       4.74116 ( 2577)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 183
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.9383 (tpt) cc_final: 0.9178 (mmm)
REVERT: A  130 ILE cc_start: 0.9718 (mp) cc_final: 0.9358 (tp)
REVERT: C   64 GLU cc_start: 0.9237 (tp30) cc_final: 0.8754 (tp30)
REVERT: E   67 PHE cc_start: 0.8915 (t80) cc_final: 0.8498 (t80)
REVERT: E   71 VAL cc_start: 0.9379 (t) cc_final: 0.9168 (t)
REVERT: E  129 ARG cc_start: 0.9778 (tpt170) cc_final: 0.9456 (tpm170)
REVERT: F   61 PHE cc_start: 0.9204 (t80) cc_final: 0.8932 (t80)
REVERT: K   55 GLN cc_start: 0.7732 (tp40) cc_final: 0.7261 (mm110)
REVERT: K  108 ASN cc_start: 0.8152 (t0) cc_final: 0.7935 (m-40)
REVERT: N  110 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8854 (tp30)
REVERT: O   93 GLN cc_start: 0.9746 (tp-100) cc_final: 0.9488 (tm-30)
REVERT: P   59 LYS cc_start: 0.8668 (mttp) cc_final: 0.8317 (mmmt)
REVERT: P   88 TYR cc_start: 0.9622 (t80) cc_final: 0.9220 (t80)
  outliers start: 1
  outliers final: 1
  residues processed: 184
  average time/residue: 0.1412
  time to fit residues: 39.0699
Evaluate side-chains
  126 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 125
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 132 optimal weight:   10.0000
   chunk 2 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 76 optimal weight:    0.9990
   chunk 137 optimal weight:    8.9990
   chunk 122 optimal weight:   10.0000
   chunk 21 optimal weight:    8.9990
   chunk 99 optimal weight:    5.9990
   chunk 80 optimal weight:    9.9990
   chunk 44 optimal weight:    4.9990
   chunk 107 optimal weight:   10.0000
   overall best weight:    3.3588

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 106 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.047050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.035257 restraints weight = 241077.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.036346 restraints weight = 142748.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.037120 restraints weight = 98204.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.037672 restraints weight = 74126.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.037971 restraints weight = 59880.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.2175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  18408  Z= 0.205
  Angle     :  0.697   7.223  26628  Z= 0.419
  Chirality :  0.038   0.154   3032
  Planarity :  0.005   0.054   1934
  Dihedral  : 33.080 168.091   6222
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 22.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.34 (0.25), residues: 1075
  helix:  0.90 (0.18), residues: 782
  sheet:  None (None), residues: 0
  loop : -1.51 (0.34), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG O 128 
 TYR   0.020   0.001   TYR P  72 
 PHE   0.033   0.002   PHE K 104 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 (18408)
  covalent geometry    : angle       0.69717 (26628)
  hydrogen bonds       : bond        0.08187 (  996)
  hydrogen bonds       : angle       4.43872 ( 2577)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 0.491 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 GLU cc_start: 0.9481 (mp0) cc_final: 0.9213 (mp0)
REVERT: C   64 GLU cc_start: 0.9187 (tp30) cc_final: 0.8748 (tp30)
REVERT: D   34 TYR cc_start: 0.8914 (m-80) cc_final: 0.8639 (m-80)
REVERT: D   65 ASP cc_start: 0.9678 (t0) cc_final: 0.9340 (t0)
REVERT: D   69 ARG cc_start: 0.9100 (mtp180) cc_final: 0.8581 (ptp-110)
REVERT: E   67 PHE cc_start: 0.8872 (t80) cc_final: 0.8433 (t80)
REVERT: E   71 VAL cc_start: 0.9401 (t) cc_final: 0.9178 (t)
REVERT: E  129 ARG cc_start: 0.9771 (tpt170) cc_final: 0.9481 (tpp-160)
REVERT: F   59 LYS cc_start: 0.9781 (tptp) cc_final: 0.9565 (tptp)
REVERT: F   61 PHE cc_start: 0.9258 (t80) cc_final: 0.9010 (t80)
REVERT: F   72 TYR cc_start: 0.9395 (m-10) cc_final: 0.9038 (m-10)
REVERT: F   92 ARG cc_start: 0.9384 (mmm160) cc_final: 0.8762 (mmm160)
REVERT: K   55 GLN cc_start: 0.7683 (tp40) cc_final: 0.7225 (mm110)
REVERT: N  110 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8619 (tp30)
REVERT: O   93 GLN cc_start: 0.9762 (tp-100) cc_final: 0.9496 (tm-30)
REVERT: P   59 LYS cc_start: 0.8733 (mttp) cc_final: 0.8437 (mmmt)
REVERT: P   88 TYR cc_start: 0.9602 (t80) cc_final: 0.9201 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 190
  average time/residue: 0.1527
  time to fit residues: 42.8096
Evaluate side-chains
  133 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 53 optimal weight:    7.9990
   chunk 85 optimal weight:    6.9990
   chunk 82 optimal weight:    0.0870
   chunk 115 optimal weight:   10.0000
   chunk 38 optimal weight:    7.9990
   chunk 83 optimal weight:    5.9990
   chunk 88 optimal weight:   20.0000
   chunk 8 optimal weight:    4.9990
   chunk 68 optimal weight:    6.9990
   chunk 75 optimal weight:    0.0870
   chunk 93 optimal weight:    0.9980
   overall best weight:    2.4340

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 106 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.048168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.036316 restraints weight = 236963.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.037426 restraints weight = 140430.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.038218 restraints weight = 96401.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.038801 restraints weight = 72531.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.039195 restraints weight = 58232.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.2540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  18408  Z= 0.185
  Angle     :  0.689   6.833  26628  Z= 0.412
  Chirality :  0.038   0.166   3032
  Planarity :  0.004   0.052   1934
  Dihedral  : 32.878 169.378   6222
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 19.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  2.17 %
    Favored  : 97.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.25), residues: 1075
  helix:  1.04 (0.18), residues: 782
  sheet:  None (None), residues: 0
  loop : -1.33 (0.35), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A  52 
 TYR   0.014   0.001   TYR P  72 
 PHE   0.035   0.002   PHE K 104 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 (18408)
  covalent geometry    : angle       0.68934 (26628)
  hydrogen bonds       : bond        0.07043 (  996)
  hydrogen bonds       : angle       4.26881 ( 2577)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 192
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.9323 (tpt) cc_final: 0.9108 (mmm)
REVERT: C   64 GLU cc_start: 0.9147 (tp30) cc_final: 0.8701 (tp30)
REVERT: D   34 TYR cc_start: 0.8898 (m-80) cc_final: 0.8568 (m-80)
REVERT: D   65 ASP cc_start: 0.9632 (t0) cc_final: 0.9406 (t0)
REVERT: D   69 ARG cc_start: 0.9143 (mtp180) cc_final: 0.8625 (ptp-110)
REVERT: F   59 LYS cc_start: 0.9781 (tptp) cc_final: 0.9491 (tptp)
REVERT: F   61 PHE cc_start: 0.9282 (t80) cc_final: 0.8981 (t80)
REVERT: F   63 GLU cc_start: 0.9232 (pp20) cc_final: 0.8740 (pp20)
REVERT: F   92 ARG cc_start: 0.9337 (mmm160) cc_final: 0.8854 (mmm-85)
REVERT: K   55 GLN cc_start: 0.7750 (tp40) cc_final: 0.7282 (mm-40)
REVERT: N  110 GLU cc_start: 0.9388 (mm-30) cc_final: 0.9180 (tp30)
REVERT: O   90 MET cc_start: 0.9657 (tpp) cc_final: 0.9455 (tpp)
REVERT: O   93 GLN cc_start: 0.9759 (tp-100) cc_final: 0.9446 (tm-30)
REVERT: P   88 TYR cc_start: 0.9594 (t80) cc_final: 0.9171 (t80)
  outliers start: 2
  outliers final: 1
  residues processed: 194
  average time/residue: 0.1496
  time to fit residues: 42.9551
Evaluate side-chains
  134 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 133
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 41 optimal weight:    7.9990
   chunk 14 optimal weight:    6.9990
   chunk 70 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   chunk 92 optimal weight:   20.0000
   chunk 37 optimal weight:    8.9990
   chunk 121 optimal weight:   10.0000
   chunk 57 optimal weight:   40.0000
   chunk 5 optimal weight:    2.9990
   chunk 94 optimal weight:    9.9990
   chunk 21 optimal weight:    9.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K  85 GLN
** M  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 106 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.045176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.033669 restraints weight = 250293.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.034706 restraints weight = 151871.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.035439 restraints weight = 105590.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.035962 restraints weight = 80036.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.036263 restraints weight = 64614.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.2716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050  18408  Z= 0.276
  Angle     :  0.745  10.233  26628  Z= 0.444
  Chirality :  0.040   0.171   3032
  Planarity :  0.006   0.063   1934
  Dihedral  : 33.307 171.125   6222
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 30.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  3.04 %
    Favored  : 96.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.31 (0.24), residues: 1075
  helix:  0.83 (0.18), residues: 764
  sheet:  None (None), residues: 0
  loop : -1.24 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  71 
 TYR   0.027   0.002   TYR P  98 
 PHE   0.039   0.003   PHE K 104 
 HIS   0.007   0.002   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00578 (18408)
  covalent geometry    : angle       0.74457 (26628)
  hydrogen bonds       : bond        0.10911 (  996)
  hydrogen bonds       : angle       4.83571 ( 2577)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 172
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 GLU cc_start: 0.9490 (mp0) cc_final: 0.9258 (mp0)
REVERT: C   61 GLU cc_start: 0.9030 (tm-30) cc_final: 0.8791 (tm-30)
REVERT: C   64 GLU cc_start: 0.9169 (tp30) cc_final: 0.8713 (tp30)
REVERT: F   59 LYS cc_start: 0.9802 (tptp) cc_final: 0.9575 (tptp)
REVERT: F   92 ARG cc_start: 0.9325 (mmm160) cc_final: 0.8827 (mmm-85)
REVERT: K   55 GLN cc_start: 0.7824 (tp40) cc_final: 0.7343 (mm-40)
REVERT: N  110 GLU cc_start: 0.9415 (mm-30) cc_final: 0.9107 (tp30)
REVERT: O   93 GLN cc_start: 0.9744 (tp-100) cc_final: 0.9339 (tm-30)
REVERT: P   59 LYS cc_start: 0.8688 (mttp) cc_final: 0.8366 (mmmt)
REVERT: P   88 TYR cc_start: 0.9578 (t80) cc_final: 0.9190 (t80)
REVERT: P   98 TYR cc_start: 0.8749 (m-80) cc_final: 0.8446 (m-80)
  outliers start: 2
  outliers final: 2
  residues processed: 174
  average time/residue: 0.1424
  time to fit residues: 37.2496
Evaluate side-chains
  120 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 118
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 32 optimal weight:    0.0040
   chunk 54 optimal weight:   20.0000
   chunk 90 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 93 optimal weight:    5.9990
   chunk 123 optimal weight:   10.0000
   chunk 21 optimal weight:    5.9990
   chunk 85 optimal weight:    5.9990
   chunk 108 optimal weight:    8.9990
   chunk 13 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.9596

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  85 GLN
** M  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  84 GLN
** M 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 106 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.049709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.037835 restraints weight = 234863.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.039027 restraints weight = 138661.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.039852 restraints weight = 94467.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.040440 restraints weight = 70829.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.040842 restraints weight = 56813.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.3278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  18408  Z= 0.171
  Angle     :  0.705   7.293  26628  Z= 0.418
  Chirality :  0.039   0.152   3032
  Planarity :  0.004   0.057   1934
  Dihedral  : 32.701 167.105   6222
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 17.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.74 %
    Favored  : 98.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.64 (0.25), residues: 1075
  helix:  1.08 (0.18), residues: 778
  sheet:  None (None), residues: 0
  loop : -1.22 (0.34), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG K  52 
 TYR   0.018   0.001   TYR E  99 
 PHE   0.034   0.002   PHE K 104 
 HIS   0.006   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 (18408)
  covalent geometry    : angle       0.70489 (26628)
  hydrogen bonds       : bond        0.05844 (  996)
  hydrogen bonds       : angle       4.09415 ( 2577)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 201
  time to evaluate  : 0.481 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.9308 (mp0) cc_final: 0.9019 (mp0)
REVERT: A  100 LEU cc_start: 0.9811 (mt) cc_final: 0.9542 (pp)
REVERT: A  120 MET cc_start: 0.9233 (tpt) cc_final: 0.9032 (mmm)
REVERT: B   84 MET cc_start: 0.9521 (ppp) cc_final: 0.9213 (ppp)
REVERT: C   61 GLU cc_start: 0.8983 (tm-30) cc_final: 0.8718 (tm-30)
REVERT: C   64 GLU cc_start: 0.9095 (tp30) cc_final: 0.8654 (tp30)
REVERT: F   59 LYS cc_start: 0.9769 (tptp) cc_final: 0.9423 (tptp)
REVERT: F   61 PHE cc_start: 0.9314 (t80) cc_final: 0.8928 (t80)
REVERT: F   63 GLU cc_start: 0.9194 (pp20) cc_final: 0.8681 (pp20)
REVERT: F   92 ARG cc_start: 0.9312 (mmm160) cc_final: 0.8791 (mmm-85)
REVERT: K   55 GLN cc_start: 0.7868 (tp40) cc_final: 0.7444 (mm-40)
REVERT: N  110 GLU cc_start: 0.9370 (mm-30) cc_final: 0.9165 (tp30)
REVERT: O   90 MET cc_start: 0.9698 (tpt) cc_final: 0.9479 (tpp)
REVERT: O   93 GLN cc_start: 0.9721 (tp-100) cc_final: 0.9273 (tm-30)
REVERT: P   88 TYR cc_start: 0.9553 (t80) cc_final: 0.9148 (t80)
  outliers start: 1
  outliers final: 1
  residues processed: 202
  average time/residue: 0.1598
  time to fit residues: 46.7314
Evaluate side-chains
  147 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 146
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 125 optimal weight:   10.0000
   chunk 121 optimal weight:   10.0000
   chunk 85 optimal weight:    6.9990
   chunk 77 optimal weight:   20.0000
   chunk 27 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 110 optimal weight:   10.0000
   chunk 95 optimal weight:   10.0000
   chunk 39 optimal weight:    0.9980
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 106 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.049196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.037297 restraints weight = 239256.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.038476 restraints weight = 142069.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.039312 restraints weight = 96585.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.039895 restraints weight = 72163.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.040306 restraints weight = 57786.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.3345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  18408  Z= 0.174
  Angle     :  0.700   7.625  26628  Z= 0.417
  Chirality :  0.038   0.169   3032
  Planarity :  0.005   0.054   1934
  Dihedral  : 32.644 170.865   6222
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 18.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.62 (0.25), residues: 1075
  helix:  1.06 (0.18), residues: 778
  sheet:  None (None), residues: 0
  loop : -1.25 (0.34), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG L  23 
 TYR   0.016   0.001   TYR P  72 
 PHE   0.043   0.002   PHE K 104 
 HIS   0.005   0.001   HIS N 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (18408)
  covalent geometry    : angle       0.70033 (26628)
  hydrogen bonds       : bond        0.06360 (  996)
  hydrogen bonds       : angle       4.13316 ( 2577)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.547 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 GLU cc_start: 0.9564 (mp0) cc_final: 0.9295 (mp0)
REVERT: A  100 LEU cc_start: 0.9799 (mt) cc_final: 0.9511 (pp)
REVERT: C   61 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8753 (tm-30)
REVERT: C   64 GLU cc_start: 0.9136 (tp30) cc_final: 0.8655 (tp30)
REVERT: D   65 ASP cc_start: 0.9659 (t0) cc_final: 0.9450 (t0)
REVERT: F   59 LYS cc_start: 0.9779 (tptp) cc_final: 0.9440 (tptp)
REVERT: F   61 PHE cc_start: 0.9260 (t80) cc_final: 0.8921 (t80)
REVERT: F   63 GLU cc_start: 0.9184 (pp20) cc_final: 0.8664 (pp20)
REVERT: F   92 ARG cc_start: 0.9317 (mmm160) cc_final: 0.8791 (mmm-85)
REVERT: K   55 GLN cc_start: 0.7984 (tp40) cc_final: 0.7483 (mm-40)
REVERT: N  110 GLU cc_start: 0.9371 (mm-30) cc_final: 0.9129 (tp30)
REVERT: O   93 GLN cc_start: 0.9713 (tp-100) cc_final: 0.9286 (tm-30)
REVERT: P   88 TYR cc_start: 0.9575 (t80) cc_final: 0.9180 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 193
  average time/residue: 0.1552
  time to fit residues: 43.7011
Evaluate side-chains
  139 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 125 optimal weight:   10.0000
   chunk 56 optimal weight:    8.9990
   chunk 12 optimal weight:    9.9990
   chunk 131 optimal weight:   10.0000
   chunk 73 optimal weight:    5.9990
   chunk 41 optimal weight:    1.9990
   chunk 81 optimal weight:    9.9990
   chunk 100 optimal weight:    6.9990
   chunk 134 optimal weight:   10.0000
   chunk 48 optimal weight:    0.6980
   overall best weight:    3.5388

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  81 ASN ** 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 = 0.3235 r_free = 0.3235 target = 0.048158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.036412 restraints weight = 244484.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.037578 restraints weight = 145740.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.038397 restraints weight = 99196.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.038967 restraints weight = 74401.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.039368 restraints weight = 59552.086|
|-----------------------------------------------------------------------------|
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.3328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  18408  Z= 0.203
  Angle     :  0.713   8.100  26628  Z= 0.425
  Chirality :  0.037   0.180   3032
  Planarity :  0.005   0.089   1934
  Dihedral  : 32.676 172.173   6222
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 21.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.59 (0.25), residues: 1075
  helix:  1.01 (0.18), residues: 778
  sheet:  None (None), residues: 0
  loop : -1.18 (0.35), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG E 131 
 TYR   0.035   0.002   TYR P  98 
 PHE   0.043   0.002   PHE K 104 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 (18408)
  covalent geometry    : angle       0.71328 (26628)
  hydrogen bonds       : bond        0.07862 (  996)
  hydrogen bonds       : angle       4.29102 ( 2577)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 ARG cc_start: 0.9364 (ptp90) cc_final: 0.8932 (tpm170)
REVERT: A   97 GLU cc_start: 0.9545 (mp0) cc_final: 0.9269 (mp0)
REVERT: C   61 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8721 (tm-30)
REVERT: C   64 GLU cc_start: 0.9182 (tp30) cc_final: 0.8681 (tp30)
REVERT: E  103 LEU cc_start: 0.9548 (mm) cc_final: 0.9312 (mm)
REVERT: F   59 LYS cc_start: 0.9790 (tptp) cc_final: 0.9502 (tptp)
REVERT: F   61 PHE cc_start: 0.9276 (t80) cc_final: 0.8990 (t80)
REVERT: F   63 GLU cc_start: 0.9179 (pp20) cc_final: 0.8669 (pp20)
REVERT: F   92 ARG cc_start: 0.9312 (mmm160) cc_final: 0.8801 (mmm-85)
REVERT: K   55 GLN cc_start: 0.7995 (tp40) cc_final: 0.7484 (mm-40)
REVERT: N  110 GLU cc_start: 0.9355 (mm-30) cc_final: 0.9137 (tp30)
REVERT: O   93 GLN cc_start: 0.9696 (tp-100) cc_final: 0.9433 (tm-30)
REVERT: P   88 TYR cc_start: 0.9584 (t80) cc_final: 0.9190 (t80)
REVERT: P   98 TYR cc_start: 0.8563 (m-80) cc_final: 0.8263 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 194
  average time/residue: 0.1568
  time to fit residues: 44.1497
Evaluate side-chains
  130 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 101 optimal weight:    5.9990
   chunk 72 optimal weight:    7.9990
   chunk 83 optimal weight:    4.9990
   chunk 22 optimal weight:   10.0000
   chunk 70 optimal weight:   10.0000
   chunk 93 optimal weight:    3.9990
   chunk 127 optimal weight:   10.0000
   chunk 142 optimal weight:   10.0000
   chunk 141 optimal weight:    6.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  85 GLN
** M  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  81 ASN ** 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 = 0.3209 r_free = 0.3209 target = 0.047009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.035391 restraints weight = 247577.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.036517 restraints weight = 148907.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.037300 restraints weight = 102008.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.037854 restraints weight = 76604.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.038249 restraints weight = 61412.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.3365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  18408  Z= 0.230
  Angle     :  0.730   7.615  26628  Z= 0.435
  Chirality :  0.039   0.227   3032
  Planarity :  0.005   0.056   1934
  Dihedral  : 32.892 172.468   6222
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 24.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.41 (0.25), residues: 1075
  helix:  0.87 (0.18), residues: 772
  sheet:  None (None), residues: 0
  loop : -1.18 (0.35), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG K  52 
 TYR   0.029   0.002   TYR P  98 
 PHE   0.045   0.002   PHE K 104 
 HIS   0.006   0.001   HIS N  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 (18408)
  covalent geometry    : angle       0.72958 (26628)
  hydrogen bonds       : bond        0.09155 (  996)
  hydrogen bonds       : angle       4.57494 ( 2577)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.557 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 ARG cc_start: 0.9375 (ptp90) cc_final: 0.8991 (tpm170)
REVERT: A   97 GLU cc_start: 0.9586 (mp0) cc_final: 0.9336 (mp0)
REVERT: C   61 GLU cc_start: 0.9160 (tm-30) cc_final: 0.8959 (tm-30)
REVERT: C   64 GLU cc_start: 0.9230 (tp30) cc_final: 0.8816 (tp30)
REVERT: D   69 ARG cc_start: 0.9229 (mtp180) cc_final: 0.9027 (ttm110)
REVERT: F   59 LYS cc_start: 0.9843 (tptp) cc_final: 0.9539 (tptp)
REVERT: F   61 PHE cc_start: 0.9425 (t80) cc_final: 0.9136 (t80)
REVERT: F   63 GLU cc_start: 0.9313 (pp20) cc_final: 0.8842 (pp20)
REVERT: K   55 GLN cc_start: 0.7922 (tp40) cc_final: 0.7409 (mm-40)
REVERT: N   56 MET cc_start: 0.9717 (ppp) cc_final: 0.9344 (ptp)
REVERT: N  110 GLU cc_start: 0.9318 (mm-30) cc_final: 0.9099 (tp30)
REVERT: O   93 GLN cc_start: 0.9763 (tp-100) cc_final: 0.9433 (tm-30)
REVERT: P   88 TYR cc_start: 0.9558 (t80) cc_final: 0.9180 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 188
  average time/residue: 0.1480
  time to fit residues: 41.1737
Evaluate side-chains
  128 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 51 optimal weight:    0.4980
   chunk 101 optimal weight:    3.9990
   chunk 71 optimal weight:    3.9990
   chunk 36 optimal weight:   30.0000
   chunk 100 optimal weight:    9.9990
   chunk 26 optimal weight:    0.0470
   chunk 139 optimal weight:   10.0000
   chunk 6 optimal weight:    5.9990
   chunk 57 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9990
   chunk 108 optimal weight:   10.0000
   overall best weight:    1.9084

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  31 HIS
** M 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  81 ASN ** 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 = 0.3257 r_free = 0.3257 target = 0.048945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.037147 restraints weight = 239414.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.038324 restraints weight = 142191.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.039152 restraints weight = 97058.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.039736 restraints weight = 72646.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.040153 restraints weight = 58128.934|
|-----------------------------------------------------------------------------|
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.3748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  18408  Z= 0.178
  Angle     :  0.710   6.790  26628  Z= 0.422
  Chirality :  0.038   0.181   3032
  Planarity :  0.005   0.056   1934
  Dihedral  : 32.680 170.728   6222
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 19.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.54 (0.25), residues: 1075
  helix:  0.94 (0.18), residues: 782
  sheet:  None (None), residues: 0
  loop : -1.11 (0.35), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG K  52 
 TYR   0.025   0.001   TYR P  98 
 PHE   0.036   0.002   PHE K 104 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 (18408)
  covalent geometry    : angle       0.71041 (26628)
  hydrogen bonds       : bond        0.06547 (  996)
  hydrogen bonds       : angle       4.28927 ( 2577)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2985.73 seconds
wall clock time: 52 minutes 38.14 seconds (3158.14 seconds total)