Starting phenix.real_space_refine
on Tue Nov 18 06:02:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6fq8_4299/11_2025/6fq8_4299.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6fq8_4299/11_2025/6fq8_4299.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6fq8_4299/11_2025/6fq8_4299.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6fq8_4299/11_2025/6fq8_4299.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6fq8_4299/11_2025/6fq8_4299.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6fq8_4299/11_2025/6fq8_4299.cif"
  }
  resolution = 4.8
  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=   0.003 sd=   0.027
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     294      5.49       5
     S      12      5.16       5
     C    6575      2.51       5
     N    2231      2.21       5
     O    2801      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11913
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 782
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 782
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
    Chain: "B"
      Number of atoms: 674
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 674
          Classifications: {'peptide': 84}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 1, 'TRANS': 82}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "C"
      Number of atoms: 809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 809
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "D"
      Number of atoms: 690
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 690
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 2, 'TRANS': 86}
    Chain: "E"
      Number of atoms: 765
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 765
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 3, 'TRANS': 89}
    Chain: "F"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "G"
      Number of atoms: 814
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 814
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 5, 'TRANS': 100}
    Chain: "H"
      Number of atoms: 690
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 690
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 2, 'TRANS': 86}
    Chain: "I"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
  Time building chain proxies: 2.82, per 1000 atoms: 0.24
  Number of scatterers: 11913
  At special positions: 0
  Unit cell: (77, 123.2, 110.6, 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      12     16.00
     P     294     15.00
     O    2801      8.00
     N    2231      7.00
     C    6575      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: 1.01
  Conformation dependent library (CDL) restraints added in 344.1 milliseconds
  

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1396

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 10 sheets defined
      75.1% alpha, 2.7% beta
      145 base pairs and 259 stacking pairs defined.
    Time for finding SS restraints: 2.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 76
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.625A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 47 through 77
      removed outlier: 4.170A  pdb=" N   TYR B  51 " --> pdb=" O   SER B  47 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   GLU B  52 " --> pdb=" O   GLY B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.563A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.374A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.726A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
      removed outlier: 3.841A  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
    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 120
      removed outlier: 3.678A  pdb=" N   ALA D 104 " --> pdb=" O   PRO D 100 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 76
      removed outlier: 3.513A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.845A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 29
      removed outlier: 3.687A  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: 4.011A  pdb=" N   TYR F  51 " --> pdb=" O   SER F  47 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   GLU F  52 " --> pdb=" O   GLY F  48 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.586A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 21
      removed outlier: 4.020A  pdb=" N   ALA G  21 " --> pdb=" O   ARG G  17 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 26 through 36
    Processing helix  chain 'G' and resid 45 through 72
      removed outlier: 4.346A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 100 through 121
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.968A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
      removed outlier: 3.653A  pdb=" N   ILE A 119 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.050A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102
      removed outlier: 7.439A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.007A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
      removed outlier: 3.817A  pdb=" N   ILE E 119 " --> pdb=" O   ARG F  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.113A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78

    404 hydrogen bonds defined for protein.
    1185 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      370 hydrogen bonds
      736 hydrogen bond angles
      0 basepair planarities
      145 basepair parallelities
      259 stacking parallelities
  Total time for adding SS restraints: 2.57

  Time building geometry restraints manager: 1.37 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: 1837
        1.33 -     1.45: 4571
        1.45 -     1.57: 5708
        1.57 -     1.69: 586
        1.69 -     1.81: 22
  Bond restraints: 12724
  Sorted by residual:
  bond pdb=" C   ARG E  42 "
       pdb=" N   PRO E  43 "
    ideal  model  delta    sigma   weight residual
    1.330  1.373 -0.043 1.19e-02 7.06e+03 1.31e+01
  bond pdb=" C3'  DG I  20 "
       pdb=" O3'  DG I  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.495 -0.073 3.00e-02 1.11e+03 5.97e+00
  bond pdb=" C   LEU E  65 "
       pdb=" N   PRO E  66 "
    ideal  model  delta    sigma   weight residual
    1.335  1.367 -0.032 1.36e-02 5.41e+03 5.41e+00
  bond pdb=" C3'  DT J  31 "
       pdb=" O3'  DT J  31 "
    ideal  model  delta    sigma   weight residual
    1.422  1.490 -0.068 3.00e-02 1.11e+03 5.06e+00
  bond pdb=" C3'  DC I  52 "
       pdb=" O3'  DC I  52 "
    ideal  model  delta    sigma   weight residual
    1.422  1.489 -0.067 3.00e-02 1.11e+03 4.98e+00
  ... (remaining 12719 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.93: 17956
        2.93 -     5.86: 450
        5.86 -     8.79: 41
        8.79 -    11.72: 6
       11.72 -    14.65: 1
  Bond angle restraints: 18454
  Sorted by residual:
  angle pdb=" N   LEU B  22 "
        pdb=" CA  LEU B  22 "
        pdb=" C   LEU B  22 "
      ideal   model   delta    sigma   weight residual
     111.17  120.49   -9.32 1.41e+00 5.03e-01 4.37e+01
  angle pdb=" O4'  DA I  26 "
        pdb=" C1'  DA I  26 "
        pdb=" N9   DA I  26 "
      ideal   model   delta    sigma   weight residual
     108.40  100.85    7.55 1.50e+00 4.44e-01 2.53e+01
  angle pdb=" C   ASP C  90 "
        pdb=" N   GLU C  91 "
        pdb=" CA  GLU C  91 "
      ideal   model   delta    sigma   weight residual
     120.82  128.36   -7.54 1.50e+00 4.44e-01 2.53e+01
  angle pdb=" OP1  DC J  10 "
        pdb=" P    DC J  10 "
        pdb=" O5'  DC J  10 "
      ideal   model   delta    sigma   weight residual
     109.00   94.35   14.65 3.00e+00 1.11e-01 2.38e+01
  angle pdb=" N   PRO E  43 "
        pdb=" CA  PRO E  43 "
        pdb=" C   PRO E  43 "
      ideal   model   delta    sigma   weight residual
     111.26  118.60   -7.34 1.63e+00 3.76e-01 2.03e+01
  ... (remaining 18449 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.58: 5446
       32.58 -    65.15: 1398
       65.15 -    97.73: 37
       97.73 -   130.30: 4
      130.30 -   162.88: 2
  Dihedral angle restraints: 6887
    sinusoidal: 4725
      harmonic: 2162
  Sorted by residual:
  dihedral pdb=" CA  VAL B  21 "
           pdb=" C   VAL B  21 "
           pdb=" N   LEU B  22 "
           pdb=" CA  LEU B  22 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.30   19.70     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" C4'  DT I -59 "
           pdb=" C3'  DT I -59 "
           pdb=" O3'  DT I -59 "
           pdb=" P    DC I -58 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   57.12  162.88     1      3.50e+01 8.16e-04 1.53e+01
  dihedral pdb=" C4'  DG I  20 "
           pdb=" C3'  DG I  20 "
           pdb=" O3'  DG I  20 "
           pdb=" P    DG I  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   59.56  160.44     1      3.50e+01 8.16e-04 1.52e+01
  ... (remaining 6884 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 1523
       0.070 -    0.140: 494
       0.140 -    0.210: 84
       0.210 -    0.280: 4
       0.280 -    0.350: 5
  Chirality restraints: 2110
  Sorted by residual:
  chirality pdb=" C1'  DG I  20 "
            pdb=" O4'  DG I  20 "
            pdb=" C2'  DG I  20 "
            pdb=" N9   DG I  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.42    2.07    0.35 2.00e-01 2.50e+01 3.07e+00
  chirality pdb=" C1'  DA J  16 "
            pdb=" O4'  DA J  16 "
            pdb=" C2'  DA J  16 "
            pdb=" N9   DA J  16 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.42    2.10    0.32 2.00e-01 2.50e+01 2.59e+00
  chirality pdb=" C1'  DT I  33 "
            pdb=" O4'  DT I  33 "
            pdb=" C2'  DT I  33 "
            pdb=" N1   DT I  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.16    0.31 2.00e-01 2.50e+01 2.43e+00
  ... (remaining 2107 not shown)

  Planarity restraints: 1313
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT I  54 "    0.061 2.00e-02 2.50e+03   2.88e-02 2.07e+01
        pdb=" N1   DT I  54 "   -0.017 2.00e-02 2.50e+03
        pdb=" C2   DT I  54 "   -0.021 2.00e-02 2.50e+03
        pdb=" O2   DT I  54 "   -0.011 2.00e-02 2.50e+03
        pdb=" N3   DT I  54 "    0.005 2.00e-02 2.50e+03
        pdb=" C4   DT I  54 "    0.012 2.00e-02 2.50e+03
        pdb=" O4   DT I  54 "    0.020 2.00e-02 2.50e+03
        pdb=" C5   DT I  54 "   -0.002 2.00e-02 2.50e+03
        pdb=" C7   DT I  54 "    0.008 2.00e-02 2.50e+03
        pdb=" C6   DT I  54 "   -0.056 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  26 "   -0.065 2.00e-02 2.50e+03   2.71e-02 2.02e+01
        pdb=" N9   DA I  26 "    0.048 2.00e-02 2.50e+03
        pdb=" C8   DA I  26 "    0.019 2.00e-02 2.50e+03
        pdb=" N7   DA I  26 "    0.007 2.00e-02 2.50e+03
        pdb=" C5   DA I  26 "   -0.004 2.00e-02 2.50e+03
        pdb=" C6   DA I  26 "   -0.006 2.00e-02 2.50e+03
        pdb=" N6   DA I  26 "   -0.028 2.00e-02 2.50e+03
        pdb=" N1   DA I  26 "    0.003 2.00e-02 2.50e+03
        pdb=" C2   DA I  26 "    0.005 2.00e-02 2.50e+03
        pdb=" N3   DA I  26 "    0.014 2.00e-02 2.50e+03
        pdb=" C4   DA I  26 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I -15 "    0.062 2.00e-02 2.50e+03   2.67e-02 1.96e+01
        pdb=" N9   DA I -15 "   -0.054 2.00e-02 2.50e+03
        pdb=" C8   DA I -15 "   -0.012 2.00e-02 2.50e+03
        pdb=" N7   DA I -15 "   -0.009 2.00e-02 2.50e+03
        pdb=" C5   DA I -15 "    0.006 2.00e-02 2.50e+03
        pdb=" C6   DA I -15 "    0.002 2.00e-02 2.50e+03
        pdb=" N6   DA I -15 "    0.025 2.00e-02 2.50e+03
        pdb=" N1   DA I -15 "    0.003 2.00e-02 2.50e+03
        pdb=" C2   DA I -15 "   -0.008 2.00e-02 2.50e+03
        pdb=" N3   DA I -15 "   -0.011 2.00e-02 2.50e+03
        pdb=" C4   DA I -15 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 1310 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2096
        2.78 -     3.31: 11080
        3.31 -     3.84: 25147
        3.84 -     4.37: 28356
        4.37 -     4.90: 39116
  Nonbonded interactions: 105795
  Sorted by model distance:
  nonbonded pdb=" OH  TYR H  39 "
            pdb=" OP2  DG J -52 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O2   DC I  61 "
            pdb=" N2   DG J -61 "
     model   vdw
     2.256 2.496
  nonbonded pdb=" O   THR G  16 "
            pdb=" OG  SER G  19 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" O   ILE B  50 "
            pdb=" OG1 THR B  54 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" OG  SER C  18 "
            pdb=" O   PHE C  25 "
     model   vdw
     2.320 3.040
  ... (remaining 105790 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' and resid 40 through 132)
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and resid 20 through 100)
  selection = (chain 'F' and resid 20 through 100)
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 13 through 117)
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.280
  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:          0.150
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     14.010
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7063
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      :  0.008   0.074  12724  Z= 0.383
  Angle     :  1.161  14.650  18454  Z= 0.684
  Chirality :  0.067   0.350   2110
  Planarity :  0.008   0.041   1313
  Dihedral  : 26.946 162.875   5491
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  1.30 %
    Favored  : 98.54 %
  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: -0.86 (0.27), residues: 728
  helix: -0.24 (0.20), residues: 502
  sheet:  None (None), residues: 0
  loop : -1.04 (0.37), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F  45 
 TYR   0.034   0.003   TYR A  41 
 PHE   0.044   0.005   PHE A 104 
 HIS   0.015   0.003   HIS G  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00843 (12724)
  covalent geometry    : angle       1.16112 (18454)
  hydrogen bonds       : bond        0.13949 (  774)
  hydrogen bonds       : angle       6.31798 ( 1921)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 223
  time to evaluate  : 0.303 
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: 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   93 GLN cc_start: 0.8963 (tt0) cc_final: 0.8090 (tp-100)
REVERT: A   94 GLU cc_start: 0.9089 (tp30) cc_final: 0.8882 (tm-30)
REVERT: A   97 GLU cc_start: 0.8655 (mt-10) cc_final: 0.7339 (mt-10)
REVERT: A  100 LEU cc_start: 0.9661 (mt) cc_final: 0.9354 (pp)
REVERT: B   31 LYS cc_start: 0.8792 (tttp) cc_final: 0.8567 (tmtt)
REVERT: B   63 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7555 (mt-10)
REVERT: B   84 MET cc_start: 0.9144 (mmt) cc_final: 0.8800 (mpp)
REVERT: C   38 ASN cc_start: 0.7504 (m-40) cc_final: 0.7171 (m-40)
REVERT: C   64 GLU cc_start: 0.9468 (tt0) cc_final: 0.9215 (tp30)
REVERT: C   92 GLU cc_start: 0.9248 (mt-10) cc_final: 0.8911 (pt0)
REVERT: D   54 LYS cc_start: 0.9408 (mttt) cc_final: 0.9087 (tmtt)
REVERT: D   99 LEU cc_start: 0.9593 (mt) cc_final: 0.9323 (tp)
REVERT: E  110 CYS cc_start: 0.8827 (m) cc_final: 0.8229 (m)
REVERT: E  124 ILE cc_start: 0.9503 (mt) cc_final: 0.9260 (mp)
REVERT: F   62 LEU cc_start: 0.9610 (mt) cc_final: 0.9193 (pp)
REVERT: F   68 ASP cc_start: 0.9423 (m-30) cc_final: 0.9172 (m-30)
REVERT: F   72 TYR cc_start: 0.9186 (m-80) cc_final: 0.8858 (m-80)
REVERT: F   81 VAL cc_start: 0.8490 (t) cc_final: 0.8280 (t)
REVERT: F   84 MET cc_start: 0.8590 (mmm) cc_final: 0.7664 (ttp)
REVERT: G   34 LEU cc_start: 0.9500 (mt) cc_final: 0.9242 (mt)
REVERT: G   36 LYS cc_start: 0.9543 (mttm) cc_final: 0.9326 (mmtm)
REVERT: G   38 ASN cc_start: 0.7500 (m110) cc_final: 0.6344 (t0)
REVERT: G   84 GLN cc_start: 0.8676 (tp40) cc_final: 0.8195 (tm-30)
REVERT: G   94 ASN cc_start: 0.8077 (t0) cc_final: 0.7819 (t0)
REVERT: H   54 LYS cc_start: 0.9309 (tptm) cc_final: 0.8979 (tptt)
REVERT: H   59 MET cc_start: 0.9382 (mmm) cc_final: 0.8791 (mmm)
REVERT: H   65 ASP cc_start: 0.8494 (t0) cc_final: 0.8261 (t70)
REVERT: H   66 VAL cc_start: 0.8933 (t) cc_final: 0.8702 (m)
REVERT: H   81 ASN cc_start: 0.9315 (m-40) cc_final: 0.8921 (p0)
REVERT: H  100 PRO cc_start: 0.8731 (Cg_exo) cc_final: 0.8510 (Cg_endo)
REVERT: H  103 LEU cc_start: 0.8697 (mt) cc_final: 0.8478 (mt)
REVERT: H  106 HIS cc_start: 0.9397 (m-70) cc_final: 0.9029 (m-70)
  outliers start: 1
  outliers final: 0
  residues processed: 224
  average time/residue: 0.1532
  time to fit residues: 44.7403
Evaluate side-chains
  137 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    7.9990
   chunk 45 optimal weight:    6.9990
   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
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  46 HIS
E  68 GLN
** E  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 110 ASN
G 112 GLN
H  46 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.046717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.039738 restraints weight = 145553.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.041076 restraints weight = 92272.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.042015 restraints weight = 64069.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.042689 restraints weight = 47595.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.043177 restraints weight = 37097.721|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.2720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.077  12724  Z= 0.268
  Angle     :  0.738   8.347  18454  Z= 0.435
  Chirality :  0.041   0.171   2110
  Planarity :  0.006   0.049   1313
  Dihedral  : 32.303 178.665   4038
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 23.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.97 %
    Favored  : 98.87 %
  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 (0.29), residues: 728
  helix:  1.00 (0.21), residues: 521
  sheet:  None (None), residues: 0
  loop : -1.05 (0.40), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG G  29 
 TYR   0.035   0.003   TYR B  98 
 PHE   0.024   0.003   PHE C  25 
 HIS   0.007   0.002   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00568 (12724)
  covalent geometry    : angle       0.73800 (18454)
  hydrogen bonds       : bond        0.08963 (  774)
  hydrogen bonds       : angle       4.18005 ( 1921)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 168
  time to evaluate  : 0.301 
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: 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: 0.9094 (tp30) cc_final: 0.8873 (tm-30)
REVERT: A  100 LEU cc_start: 0.9814 (mt) cc_final: 0.9503 (mt)
REVERT: B   62 LEU cc_start: 0.9508 (mm) cc_final: 0.9163 (mm)
REVERT: B   63 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7815 (mt-10)
REVERT: B   84 MET cc_start: 0.9246 (mmt) cc_final: 0.8902 (mpp)
REVERT: B   97 LEU cc_start: 0.8592 (tp) cc_final: 0.8086 (tp)
REVERT: C   38 ASN cc_start: 0.7368 (m-40) cc_final: 0.7036 (m-40)
REVERT: C   64 GLU cc_start: 0.9457 (tt0) cc_final: 0.9203 (tp30)
REVERT: C   68 ASN cc_start: 0.9281 (m-40) cc_final: 0.9009 (m110)
REVERT: D   77 LEU cc_start: 0.9405 (tp) cc_final: 0.9159 (tp)
REVERT: D   96 ARG cc_start: 0.8159 (mtm180) cc_final: 0.7893 (mtt180)
REVERT: D   99 LEU cc_start: 0.9380 (mt) cc_final: 0.9033 (tp)
REVERT: E  104 PHE cc_start: 0.8920 (m-80) cc_final: 0.8711 (m-80)
REVERT: E  110 CYS cc_start: 0.9012 (m) cc_final: 0.8319 (m)
REVERT: F   68 ASP cc_start: 0.9574 (m-30) cc_final: 0.9062 (m-30)
REVERT: F   72 TYR cc_start: 0.9347 (m-80) cc_final: 0.8918 (m-80)
REVERT: F   84 MET cc_start: 0.8594 (mmm) cc_final: 0.7935 (ppp)
REVERT: G   38 ASN cc_start: 0.8004 (m110) cc_final: 0.6793 (t0)
REVERT: G   84 GLN cc_start: 0.8186 (tp40) cc_final: 0.7654 (tm-30)
REVERT: G   94 ASN cc_start: 0.7908 (t0) cc_final: 0.7600 (t0)
REVERT: H   54 LYS cc_start: 0.9208 (tptm) cc_final: 0.8861 (tptt)
REVERT: H   59 MET cc_start: 0.9401 (mmm) cc_final: 0.9007 (mmm)
REVERT: H   81 ASN cc_start: 0.9134 (m-40) cc_final: 0.8823 (p0)
REVERT: H  100 PRO cc_start: 0.8688 (Cg_exo) cc_final: 0.8353 (Cg_endo)
REVERT: H  103 LEU cc_start: 0.8783 (mt) cc_final: 0.8492 (mt)
REVERT: H  106 HIS cc_start: 0.9692 (m-70) cc_final: 0.9017 (m-70)
  outliers start: 1
  outliers final: 0
  residues processed: 169
  average time/residue: 0.1278
  time to fit residues: 29.0815
Evaluate side-chains
  120 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 23 optimal weight:    9.9990
   chunk 49 optimal weight:    2.9990
   chunk 70 optimal weight:   10.0000
   chunk 84 optimal weight:   10.0000
   chunk 25 optimal weight:    0.9980
   chunk 56 optimal weight:    7.9990
   chunk 61 optimal weight:   30.0000
   chunk 29 optimal weight:    7.9990
   chunk 8 optimal weight:    7.9990
   chunk 38 optimal weight:    8.9990
   chunk 17 optimal weight:   10.0000
   overall best weight:    5.5988

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  27 GLN
** G  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  79 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.047553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.041163 restraints weight = 155339.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.042527 restraints weight = 96419.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.043487 restraints weight = 65456.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.044225 restraints weight = 47644.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.044781 restraints weight = 35839.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.3737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068  12724  Z= 0.250
  Angle     :  0.713   9.884  18454  Z= 0.421
  Chirality :  0.040   0.230   2110
  Planarity :  0.006   0.053   1313
  Dihedral  : 32.629 179.658   4038
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 21.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  1.94 %
    Favored  : 97.89 %
  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:  0.80 (0.30), residues: 728
  helix:  1.20 (0.21), residues: 522
  sheet:  None (None), residues: 0
  loop : -1.13 (0.40), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  67 
 TYR   0.022   0.002   TYR F  72 
 PHE   0.021   0.002   PHE A 104 
 HIS   0.005   0.002   HIS G  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00531 (12724)
  covalent geometry    : angle       0.71256 (18454)
  hydrogen bonds       : bond        0.08378 (  774)
  hydrogen bonds       : angle       3.99791 ( 1921)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 150
  time to evaluate  : 0.246 
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: 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   93 GLN cc_start: 0.9226 (tt0) cc_final: 0.8870 (tp-100)
REVERT: A   94 GLU cc_start: 0.9338 (tp30) cc_final: 0.9087 (tm-30)
REVERT: A  100 LEU cc_start: 0.9836 (mt) cc_final: 0.9617 (mt)
REVERT: A  104 PHE cc_start: 0.9638 (m-80) cc_final: 0.9338 (m-80)
REVERT: A  108 ASN cc_start: 0.8999 (t0) cc_final: 0.8697 (m-40)
REVERT: B   63 GLU cc_start: 0.8365 (mt-10) cc_final: 0.7930 (mt-10)
REVERT: B   68 ASP cc_start: 0.9571 (m-30) cc_final: 0.9244 (m-30)
REVERT: B   84 MET cc_start: 0.9209 (mmt) cc_final: 0.8879 (mpp)
REVERT: B   97 LEU cc_start: 0.8987 (tp) cc_final: 0.8420 (tp)
REVERT: C   64 GLU cc_start: 0.9533 (tt0) cc_final: 0.9255 (tp30)
REVERT: C   68 ASN cc_start: 0.9343 (m-40) cc_final: 0.9106 (m110)
REVERT: D   54 LYS cc_start: 0.9487 (mttt) cc_final: 0.9087 (tptp)
REVERT: D   99 LEU cc_start: 0.9400 (mt) cc_final: 0.9013 (tp)
REVERT: E   92 LEU cc_start: 0.8778 (mt) cc_final: 0.8537 (mt)
REVERT: E   94 GLU cc_start: 0.9191 (mm-30) cc_final: 0.8899 (mm-30)
REVERT: E  110 CYS cc_start: 0.9035 (m) cc_final: 0.8336 (m)
REVERT: F   72 TYR cc_start: 0.9361 (m-80) cc_final: 0.8852 (m-80)
REVERT: F   81 VAL cc_start: 0.9140 (t) cc_final: 0.8857 (t)
REVERT: F   84 MET cc_start: 0.8637 (mmm) cc_final: 0.8028 (ppp)
REVERT: G   84 GLN cc_start: 0.8189 (tp40) cc_final: 0.7314 (tm-30)
REVERT: G   94 ASN cc_start: 0.7905 (t0) cc_final: 0.7660 (t0)
REVERT: H   54 LYS cc_start: 0.9062 (tptm) cc_final: 0.8753 (tptt)
REVERT: H   59 MET cc_start: 0.9501 (mmm) cc_final: 0.9057 (mmm)
REVERT: H   81 ASN cc_start: 0.9046 (m-40) cc_final: 0.8817 (p0)
REVERT: H  100 PRO cc_start: 0.8430 (Cg_exo) cc_final: 0.7652 (Cg_endo)
REVERT: H  103 LEU cc_start: 0.8897 (mt) cc_final: 0.8385 (pp)
REVERT: H  106 HIS cc_start: 0.9743 (m-70) cc_final: 0.9193 (m-70)
  outliers start: 1
  outliers final: 0
  residues processed: 151
  average time/residue: 0.1443
  time to fit residues: 29.2745
Evaluate side-chains
  118 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 72 optimal weight:   10.0000
   chunk 22 optimal weight:    5.9990
   chunk 83 optimal weight:   10.0000
   chunk 68 optimal weight:    6.9990
   chunk 87 optimal weight:   10.0000
   chunk 25 optimal weight:   10.0000
   chunk 67 optimal weight:    8.9990
   chunk 31 optimal weight:    9.9990
   chunk 21 optimal weight:    5.9990
   chunk 13 optimal weight:    6.9990
   chunk 79 optimal weight:   10.0000
   overall best weight:    6.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  68 ASN
** G  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  84 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.042037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.035753 restraints weight = 154355.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.036993 restraints weight = 97599.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.037871 restraints weight = 67184.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.038511 restraints weight = 49209.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.039005 restraints weight = 38017.024|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.4741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.076  12724  Z= 0.299
  Angle     :  0.750  12.185  18454  Z= 0.443
  Chirality :  0.042   0.180   2110
  Planarity :  0.006   0.056   1313
  Dihedral  : 33.207 179.815   4038
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 26.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  1.78 %
    Favored  : 98.06 %
  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:  0.61 (0.30), residues: 728
  helix:  1.15 (0.22), residues: 513
  sheet:  None (None), residues: 0
  loop : -1.36 (0.40), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G  42 
 TYR   0.035   0.003   TYR B  72 
 PHE   0.023   0.003   PHE E 104 
 HIS   0.006   0.002   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00633 (12724)
  covalent geometry    : angle       0.74969 (18454)
  hydrogen bonds       : bond        0.10336 (  774)
  hydrogen bonds       : angle       4.25532 ( 1921)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 139
  time to evaluate  : 0.339 
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: 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   93 GLN cc_start: 0.9134 (tt0) cc_final: 0.8680 (tp-100)
REVERT: A   94 GLU cc_start: 0.9252 (tp30) cc_final: 0.8959 (tm-30)
REVERT: B   63 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7825 (mt-10)
REVERT: B   84 MET cc_start: 0.9214 (mmt) cc_final: 0.8840 (mpp)
REVERT: B   97 LEU cc_start: 0.8895 (tp) cc_final: 0.8336 (tp)
REVERT: C   59 THR cc_start: 0.9356 (m) cc_final: 0.9156 (p)
REVERT: C   64 GLU cc_start: 0.9472 (tt0) cc_final: 0.9146 (tp30)
REVERT: C   68 ASN cc_start: 0.9336 (m110) cc_final: 0.9084 (m110)
REVERT: C   94 ASN cc_start: 0.8998 (t0) cc_final: 0.8772 (t0)
REVERT: D   54 LYS cc_start: 0.9550 (mttt) cc_final: 0.9177 (tptp)
REVERT: D   56 MET cc_start: 0.5753 (tpt) cc_final: 0.4543 (tpt)
REVERT: E   92 LEU cc_start: 0.8884 (mt) cc_final: 0.8661 (mt)
REVERT: E  110 CYS cc_start: 0.8885 (m) cc_final: 0.8125 (m)
REVERT: F   72 TYR cc_start: 0.9417 (m-80) cc_final: 0.8798 (m-80)
REVERT: F   81 VAL cc_start: 0.8963 (t) cc_final: 0.8538 (t)
REVERT: G   84 GLN cc_start: 0.8295 (tp-100) cc_final: 0.7300 (tm-30)
REVERT: G   94 ASN cc_start: 0.7995 (t0) cc_final: 0.7699 (t0)
REVERT: H   54 LYS cc_start: 0.9184 (tptm) cc_final: 0.8859 (tptt)
REVERT: H   59 MET cc_start: 0.9383 (mmm) cc_final: 0.8962 (mmm)
REVERT: H  100 PRO cc_start: 0.8461 (Cg_exo) cc_final: 0.8001 (Cg_endo)
REVERT: H  103 LEU cc_start: 0.8910 (mt) cc_final: 0.8177 (mt)
REVERT: H  106 HIS cc_start: 0.9730 (m-70) cc_final: 0.9274 (m-70)
  outliers start: 1
  outliers final: 0
  residues processed: 140
  average time/residue: 0.1332
  time to fit residues: 25.4998
Evaluate side-chains
  104 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 63 optimal weight:   30.0000
   chunk 88 optimal weight:   10.0000
   chunk 28 optimal weight:    0.5980
   chunk 44 optimal weight:    4.9990
   chunk 56 optimal weight:    3.9990
   chunk 0 optimal weight:   30.0000
   chunk 20 optimal weight:    6.9990
   chunk 93 optimal weight:   10.0000
   chunk 43 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   overall best weight:    3.5188

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  73 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 = 0.3252 r_free = 0.3252 target = 0.043762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.036936 restraints weight = 153181.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.038233 restraints weight = 97217.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.039152 restraints weight = 67739.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.039833 restraints weight = 50348.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.040348 restraints weight = 39246.190|
|-----------------------------------------------------------------------------|
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.4798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  12724  Z= 0.207
  Angle     :  0.675  12.289  18454  Z= 0.400
  Chirality :  0.039   0.173   2110
  Planarity :  0.005   0.057   1313
  Dihedral  : 33.056 179.004   4038
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 18.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  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:  1.09 (0.30), residues: 728
  helix:  1.55 (0.22), residues: 511
  sheet:  None (None), residues: 0
  loop : -1.29 (0.38), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  17 
 TYR   0.028   0.002   TYR B  72 
 PHE   0.013   0.002   PHE A 104 
 HIS   0.005   0.002   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 (12724)
  covalent geometry    : angle       0.67466 (18454)
  hydrogen bonds       : bond        0.06947 (  774)
  hydrogen bonds       : angle       3.78126 ( 1921)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.316 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.9262 (tt0) cc_final: 0.8867 (tp-100)
REVERT: A   94 GLU cc_start: 0.9302 (tp30) cc_final: 0.8984 (tm-30)
REVERT: A  100 LEU cc_start: 0.9805 (mt) cc_final: 0.9573 (mt)
REVERT: B   54 THR cc_start: 0.9739 (m) cc_final: 0.9406 (p)
REVERT: B   63 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7783 (mt-10)
REVERT: B   84 MET cc_start: 0.9165 (mmt) cc_final: 0.8802 (mpp)
REVERT: B   97 LEU cc_start: 0.8987 (tp) cc_final: 0.8330 (tp)
REVERT: C   64 GLU cc_start: 0.9506 (tt0) cc_final: 0.9171 (tp30)
REVERT: C   68 ASN cc_start: 0.9425 (m110) cc_final: 0.9134 (m110)
REVERT: D   54 LYS cc_start: 0.9539 (mttt) cc_final: 0.9149 (tptm)
REVERT: D   77 LEU cc_start: 0.9513 (tp) cc_final: 0.9312 (tp)
REVERT: D   90 GLU cc_start: 0.8402 (mp0) cc_final: 0.8185 (mp0)
REVERT: E   92 LEU cc_start: 0.8785 (mt) cc_final: 0.8569 (mt)
REVERT: E  106 ASP cc_start: 0.9514 (t0) cc_final: 0.9087 (m-30)
REVERT: E  110 CYS cc_start: 0.9074 (m) cc_final: 0.8401 (m)
REVERT: F   58 LEU cc_start: 0.9497 (tp) cc_final: 0.9120 (pp)
REVERT: F   72 TYR cc_start: 0.9288 (m-80) cc_final: 0.8574 (m-80)
REVERT: F   81 VAL cc_start: 0.8787 (t) cc_final: 0.8517 (t)
REVERT: F   84 MET cc_start: 0.7806 (mmp) cc_final: 0.7397 (ttp)
REVERT: F  100 PHE cc_start: 0.8231 (m-80) cc_final: 0.7643 (m-80)
REVERT: G   94 ASN cc_start: 0.8003 (t0) cc_final: 0.7727 (m-40)
REVERT: H   54 LYS cc_start: 0.9131 (tptm) cc_final: 0.8812 (tptt)
REVERT: H   59 MET cc_start: 0.9433 (mmm) cc_final: 0.8945 (mmm)
REVERT: H  100 PRO cc_start: 0.8042 (Cg_exo) cc_final: 0.7401 (Cg_endo)
REVERT: H  103 LEU cc_start: 0.8700 (mt) cc_final: 0.8032 (mt)
REVERT: H  106 HIS cc_start: 0.9755 (m-70) cc_final: 0.9259 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.1370
  time to fit residues: 25.7548
Evaluate side-chains
  105 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 2 optimal weight:   30.0000
   chunk 12 optimal weight:    8.9990
   chunk 94 optimal weight:   10.0000
   chunk 13 optimal weight:    8.9990
   chunk 43 optimal weight:    0.3980
   chunk 0 optimal weight:   40.0000
   chunk 52 optimal weight:   10.0000
   chunk 11 optimal weight:    9.9990
   chunk 83 optimal weight:   10.0000
   chunk 90 optimal weight:   10.0000
   chunk 23 optimal weight:    8.9990
   overall best weight:    7.4788

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  81 ASN
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.040952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.034720 restraints weight = 156062.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.035947 restraints weight = 99635.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.036816 restraints weight = 68936.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.037446 restraints weight = 50630.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.037906 restraints weight = 39071.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.5528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.072  12724  Z= 0.305
  Angle     :  0.765  12.350  18454  Z= 0.452
  Chirality :  0.042   0.169   2110
  Planarity :  0.006   0.057   1313
  Dihedral  : 33.520 178.667   4038
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 27.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  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:  0.45 (0.30), residues: 728
  helix:  1.12 (0.22), residues: 509
  sheet:  None (None), residues: 0
  loop : -1.63 (0.39), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  63 
 TYR   0.023   0.003   TYR C  57 
 PHE   0.018   0.003   PHE D  62 
 HIS   0.005   0.002   HIS C  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00648 (12724)
  covalent geometry    : angle       0.76458 (18454)
  hydrogen bonds       : bond        0.10574 (  774)
  hydrogen bonds       : angle       4.33021 ( 1921)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.323 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.9107 (tt0) cc_final: 0.8826 (tp-100)
REVERT: A   94 GLU cc_start: 0.9471 (tp30) cc_final: 0.9194 (tm-30)
REVERT: A  100 LEU cc_start: 0.9795 (mt) cc_final: 0.9509 (mt)
REVERT: B   84 MET cc_start: 0.9198 (mmt) cc_final: 0.8822 (mpp)
REVERT: B   97 LEU cc_start: 0.9030 (tp) cc_final: 0.8490 (tp)
REVERT: C   64 GLU cc_start: 0.9483 (tt0) cc_final: 0.9194 (tp30)
REVERT: C   94 ASN cc_start: 0.9044 (t0) cc_final: 0.8801 (t0)
REVERT: D   54 LYS cc_start: 0.9541 (mttt) cc_final: 0.9166 (tptm)
REVERT: D   56 MET cc_start: 0.5879 (tpt) cc_final: 0.4710 (tpt)
REVERT: E  110 CYS cc_start: 0.8979 (m) cc_final: 0.8156 (m)
REVERT: F   72 TYR cc_start: 0.9355 (m-80) cc_final: 0.8806 (m-80)
REVERT: F   84 MET cc_start: 0.7910 (mmp) cc_final: 0.7363 (ttp)
REVERT: G   94 ASN cc_start: 0.8024 (t0) cc_final: 0.7748 (m-40)
REVERT: H   54 LYS cc_start: 0.9177 (tptm) cc_final: 0.8884 (tttm)
REVERT: H   59 MET cc_start: 0.9434 (mmm) cc_final: 0.9031 (mmm)
REVERT: H  100 PRO cc_start: 0.8207 (Cg_exo) cc_final: 0.7954 (Cg_endo)
REVERT: H  103 LEU cc_start: 0.8631 (mt) cc_final: 0.8178 (mt)
REVERT: H  106 HIS cc_start: 0.9800 (m-70) cc_final: 0.9286 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1402
  time to fit residues: 23.7619
Evaluate side-chains
  93 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 47 optimal weight:    9.9990
   chunk 9 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   chunk 93 optimal weight:   10.0000
   chunk 10 optimal weight:    5.9990
   chunk 43 optimal weight:    1.9990
   chunk 77 optimal weight:   10.0000
   chunk 48 optimal weight:    5.9990
   chunk 91 optimal weight:   10.0000
   chunk 31 optimal weight:    5.9990
   chunk 80 optimal weight:    8.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  68 ASN
D  81 ASN
E  85 GLN
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.041575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.035203 restraints weight = 154672.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.036390 restraints weight = 100565.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.037263 restraints weight = 71053.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.037895 restraints weight = 53040.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.038370 restraints weight = 41503.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.5633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067  12724  Z= 0.229
  Angle     :  0.707  12.757  18454  Z= 0.419
  Chirality :  0.041   0.166   2110
  Planarity :  0.005   0.057   1313
  Dihedral  : 33.477 179.553   4038
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 21.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  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:  0.77 (0.30), residues: 728
  helix:  1.36 (0.22), residues: 510
  sheet:  None (None), residues: 0
  loop : -1.52 (0.39), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG G  42 
 TYR   0.027   0.002   TYR B  72 
 PHE   0.043   0.003   PHE A 104 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 (12724)
  covalent geometry    : angle       0.70746 (18454)
  hydrogen bonds       : bond        0.08020 (  774)
  hydrogen bonds       : angle       4.03980 ( 1921)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.274 
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   93 GLN cc_start: 0.9188 (tt0) cc_final: 0.8119 (tp-100)
REVERT: A   94 GLU cc_start: 0.9433 (tp30) cc_final: 0.9134 (tm-30)
REVERT: A   97 GLU cc_start: 0.9189 (mt-10) cc_final: 0.7583 (mt-10)
REVERT: A  108 ASN cc_start: 0.8823 (m110) cc_final: 0.8608 (m-40)
REVERT: B   63 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7669 (mt-10)
REVERT: B   84 MET cc_start: 0.9163 (mmt) cc_final: 0.8776 (mpp)
REVERT: B   97 LEU cc_start: 0.9018 (tp) cc_final: 0.8365 (tp)
REVERT: B   98 TYR cc_start: 0.8598 (m-10) cc_final: 0.8140 (m-10)
REVERT: C   64 GLU cc_start: 0.9511 (tt0) cc_final: 0.9157 (tp30)
REVERT: C   68 ASN cc_start: 0.9418 (m-40) cc_final: 0.9116 (m110)
REVERT: C   94 ASN cc_start: 0.8929 (t0) cc_final: 0.8674 (t0)
REVERT: D   54 LYS cc_start: 0.9565 (mttt) cc_final: 0.9192 (tptm)
REVERT: D   99 LEU cc_start: 0.9199 (mm) cc_final: 0.8923 (mm)
REVERT: E   92 LEU cc_start: 0.8790 (mt) cc_final: 0.8549 (mt)
REVERT: E  110 CYS cc_start: 0.9105 (m) cc_final: 0.8211 (m)
REVERT: E  123 ASP cc_start: 0.9265 (m-30) cc_final: 0.9007 (m-30)
REVERT: F   72 TYR cc_start: 0.9306 (m-80) cc_final: 0.8672 (m-80)
REVERT: F   84 MET cc_start: 0.7709 (mmp) cc_final: 0.7296 (ttp)
REVERT: G   94 ASN cc_start: 0.8068 (t0) cc_final: 0.7748 (m-40)
REVERT: H   54 LYS cc_start: 0.9247 (tptm) cc_final: 0.8940 (tptt)
REVERT: H   59 MET cc_start: 0.9364 (mmm) cc_final: 0.8997 (mmm)
REVERT: H  100 PRO cc_start: 0.8169 (Cg_exo) cc_final: 0.7691 (Cg_endo)
REVERT: H  103 LEU cc_start: 0.8479 (mt) cc_final: 0.8087 (mt)
REVERT: H  106 HIS cc_start: 0.9762 (m-70) cc_final: 0.9237 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.1371
  time to fit residues: 23.2620
Evaluate side-chains
  95 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   chunk 81 optimal weight:   10.0000
   chunk 17 optimal weight:    0.8980
   chunk 15 optimal weight:   20.0000
   chunk 8 optimal weight:    0.1980
   chunk 18 optimal weight:    8.9990
   chunk 49 optimal weight:    7.9990
   chunk 86 optimal weight:   10.0000
   chunk 66 optimal weight:    9.9990
   chunk 1 optimal weight:    5.9990
   overall best weight:    2.4184

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 104 GLN
E  85 GLN
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.047420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.041063 restraints weight = 149633.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.042340 restraints weight = 95323.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.043339 restraints weight = 66910.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.044030 restraints weight = 48752.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.044577 restraints weight = 37220.532|
|-----------------------------------------------------------------------------|
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.5755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  12724  Z= 0.185
  Angle     :  0.677  12.095  18454  Z= 0.399
  Chirality :  0.040   0.186   2110
  Planarity :  0.005   0.056   1313
  Dihedral  : 33.155 178.019   4038
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 17.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  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:  1.01 (0.30), residues: 728
  helix:  1.61 (0.22), residues: 506
  sheet:  None (None), residues: 0
  loop : -1.57 (0.38), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  89 
 TYR   0.015   0.002   TYR C  50 
 PHE   0.035   0.002   PHE A 104 
 HIS   0.004   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 (12724)
  covalent geometry    : angle       0.67665 (18454)
  hydrogen bonds       : bond        0.06027 (  774)
  hydrogen bonds       : angle       3.77063 ( 1921)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.344 
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   93 GLN cc_start: 0.9348 (tt0) cc_final: 0.9098 (tp-100)
REVERT: A   94 GLU cc_start: 0.9476 (tp30) cc_final: 0.9132 (tm-30)
REVERT: B   63 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7589 (mt-10)
REVERT: B   71 THR cc_start: 0.9089 (p) cc_final: 0.8874 (p)
REVERT: B   84 MET cc_start: 0.9085 (mmt) cc_final: 0.8755 (mpp)
REVERT: B   92 ARG cc_start: 0.7996 (tmt170) cc_final: 0.7712 (tmm160)
REVERT: B   97 LEU cc_start: 0.8942 (tp) cc_final: 0.8270 (tp)
REVERT: B   98 TYR cc_start: 0.8875 (m-10) cc_final: 0.8558 (m-10)
REVERT: C   64 GLU cc_start: 0.9533 (tt0) cc_final: 0.9180 (tp30)
REVERT: C   68 ASN cc_start: 0.9443 (m-40) cc_final: 0.9144 (m110)
REVERT: C   94 ASN cc_start: 0.8977 (t0) cc_final: 0.8771 (m-40)
REVERT: D   54 LYS cc_start: 0.9554 (mttt) cc_final: 0.9170 (tptm)
REVERT: E   92 LEU cc_start: 0.8696 (mt) cc_final: 0.8469 (mt)
REVERT: E  106 ASP cc_start: 0.9577 (t0) cc_final: 0.8969 (m-30)
REVERT: E  110 CYS cc_start: 0.9142 (m) cc_final: 0.8220 (m)
REVERT: E  123 ASP cc_start: 0.9330 (m-30) cc_final: 0.9090 (m-30)
REVERT: F   72 TYR cc_start: 0.9273 (m-80) cc_final: 0.8658 (m-80)
REVERT: F   84 MET cc_start: 0.7735 (mmp) cc_final: 0.7385 (ttp)
REVERT: G   36 LYS cc_start: 0.9550 (mppt) cc_final: 0.9350 (mmtm)
REVERT: G   57 TYR cc_start: 0.8418 (t80) cc_final: 0.7847 (t80)
REVERT: G   94 ASN cc_start: 0.7992 (t0) cc_final: 0.7669 (m-40)
REVERT: H   54 LYS cc_start: 0.9102 (tptm) cc_final: 0.8782 (tptt)
REVERT: H   59 MET cc_start: 0.9393 (mmm) cc_final: 0.9045 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.1400
  time to fit residues: 25.4311
Evaluate side-chains
  95 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 91 optimal weight:   10.0000
   chunk 11 optimal weight:   20.0000
   chunk 19 optimal weight:    0.7980
   chunk 51 optimal weight:   20.0000
   chunk 81 optimal weight:   10.0000
   chunk 17 optimal weight:    5.9990
   chunk 41 optimal weight:    1.9990
   chunk 97 optimal weight:   10.0000
   chunk 26 optimal weight:   30.0000
   chunk 84 optimal weight:   10.0000
   chunk 85 optimal weight:   10.0000
   overall best weight:    5.7592

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  79 HIS
D  81 ASN
E  85 GLN
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.041386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.035055 restraints weight = 155719.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.036222 restraints weight = 101142.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.037088 restraints weight = 71757.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.037697 restraints weight = 53775.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.038179 restraints weight = 42391.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.6179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069  12724  Z= 0.253
  Angle     :  0.729  12.727  18454  Z= 0.429
  Chirality :  0.041   0.166   2110
  Planarity :  0.005   0.068   1313
  Dihedral  : 33.480 179.423   4038
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 24.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.87 (0.30), residues: 728
  helix:  1.44 (0.22), residues: 513
  sheet:  None (None), residues: 0
  loop : -1.57 (0.38), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG G  42 
 TYR   0.040   0.003   TYR B  72 
 PHE   0.045   0.003   PHE A 104 
 HIS   0.005   0.002   HIS H 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00540 (12724)
  covalent geometry    : angle       0.72891 (18454)
  hydrogen bonds       : bond        0.08737 (  774)
  hydrogen bonds       : angle       4.10334 ( 1921)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.326 
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: A   93 GLN cc_start: 0.9209 (tt0) cc_final: 0.8815 (tp-100)
REVERT: A   94 GLU cc_start: 0.9437 (tp30) cc_final: 0.9132 (tm-30)
REVERT: A  108 ASN cc_start: 0.8854 (m110) cc_final: 0.8648 (m-40)
REVERT: B   63 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7619 (mt-10)
REVERT: B   84 MET cc_start: 0.9125 (mmt) cc_final: 0.8773 (mpp)
REVERT: B   97 LEU cc_start: 0.8885 (tp) cc_final: 0.8313 (tp)
REVERT: C   64 GLU cc_start: 0.9490 (tt0) cc_final: 0.9175 (tp30)
REVERT: C   68 ASN cc_start: 0.9435 (m-40) cc_final: 0.9158 (m110)
REVERT: C   94 ASN cc_start: 0.8987 (t0) cc_final: 0.8745 (t0)
REVERT: D   54 LYS cc_start: 0.9561 (mttt) cc_final: 0.9208 (tptm)
REVERT: E   90 MET cc_start: 0.9487 (mmp) cc_final: 0.9268 (mtt)
REVERT: E   92 LEU cc_start: 0.8758 (mt) cc_final: 0.8547 (mt)
REVERT: E  110 CYS cc_start: 0.9094 (m) cc_final: 0.8227 (m)
REVERT: E  123 ASP cc_start: 0.9258 (m-30) cc_final: 0.8958 (m-30)
REVERT: F   62 LEU cc_start: 0.9639 (mt) cc_final: 0.9321 (pp)
REVERT: F   72 TYR cc_start: 0.9311 (m-80) cc_final: 0.8721 (m-80)
REVERT: F   84 MET cc_start: 0.7683 (mmp) cc_final: 0.7266 (ttp)
REVERT: G   94 ASN cc_start: 0.8092 (t0) cc_final: 0.7796 (m-40)
REVERT: H   54 LYS cc_start: 0.9260 (tptm) cc_final: 0.8950 (tptt)
REVERT: H   59 MET cc_start: 0.9373 (mmm) cc_final: 0.9011 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1449
  time to fit residues: 23.7580
Evaluate side-chains
  91 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 14 optimal weight:    8.9990
   chunk 62 optimal weight:    3.9990
   chunk 15 optimal weight:   20.0000
   chunk 31 optimal weight:   20.0000
   chunk 97 optimal weight:   10.0000
   chunk 50 optimal weight:    5.9990
   chunk 24 optimal weight:    8.9990
   chunk 9 optimal weight:    7.9990
   chunk 72 optimal weight:   10.0000
   chunk 0 optimal weight:   30.0000
   chunk 40 optimal weight:    6.9990
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  85 GLN
G 110 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.040668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.034384 restraints weight = 157782.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.035599 restraints weight = 100803.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.036477 restraints weight = 70303.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.037109 restraints weight = 51994.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.037583 restraints weight = 40397.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.6619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070  12724  Z= 0.285
  Angle     :  0.766  12.762  18454  Z= 0.450
  Chirality :  0.043   0.175   2110
  Planarity :  0.006   0.068   1313
  Dihedral  : 33.918 177.819   4038
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 27.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  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:  0.35 (0.29), residues: 728
  helix:  1.10 (0.22), residues: 510
  sheet:  None (None), residues: 0
  loop : -1.86 (0.38), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG G  42 
 TYR   0.030   0.003   TYR B  72 
 PHE   0.041   0.004   PHE A 104 
 HIS   0.006   0.002   HIS D  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00610 (12724)
  covalent geometry    : angle       0.76571 (18454)
  hydrogen bonds       : bond        0.10081 (  774)
  hydrogen bonds       : angle       4.30366 ( 1921)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.322 
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: A   93 GLN cc_start: 0.9121 (tt0) cc_final: 0.8243 (tp-100)
REVERT: A   94 GLU cc_start: 0.9462 (tp30) cc_final: 0.9178 (tm-30)
REVERT: A   97 GLU cc_start: 0.9201 (mt-10) cc_final: 0.7716 (mt-10)
REVERT: A  108 ASN cc_start: 0.8890 (m110) cc_final: 0.8627 (m-40)
REVERT: B   62 LEU cc_start: 0.9573 (mm) cc_final: 0.9324 (mm)
REVERT: B   84 MET cc_start: 0.9194 (mmt) cc_final: 0.8759 (mpp)
REVERT: B   97 LEU cc_start: 0.8908 (tp) cc_final: 0.8178 (tp)
REVERT: B   98 TYR cc_start: 0.8813 (m-10) cc_final: 0.8412 (m-80)
REVERT: C   64 GLU cc_start: 0.9484 (tt0) cc_final: 0.9181 (tp30)
REVERT: C   68 ASN cc_start: 0.9438 (m-40) cc_final: 0.9178 (m110)
REVERT: C   94 ASN cc_start: 0.8996 (t0) cc_final: 0.8758 (t0)
REVERT: D   54 LYS cc_start: 0.9555 (mttt) cc_final: 0.9180 (tptm)
REVERT: E  110 CYS cc_start: 0.9011 (m) cc_final: 0.7995 (m)
REVERT: E  123 ASP cc_start: 0.9191 (m-30) cc_final: 0.8820 (m-30)
REVERT: F   62 LEU cc_start: 0.9628 (mt) cc_final: 0.9296 (pp)
REVERT: F   72 TYR cc_start: 0.9298 (m-80) cc_final: 0.8834 (m-80)
REVERT: F   84 MET cc_start: 0.7721 (mmp) cc_final: 0.7378 (ttp)
REVERT: G   94 ASN cc_start: 0.8037 (t0) cc_final: 0.7695 (t0)
REVERT: H   54 LYS cc_start: 0.9259 (tptm) cc_final: 0.8935 (tttm)
REVERT: H   59 MET cc_start: 0.9386 (mmm) cc_final: 0.9059 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.1272
  time to fit residues: 20.5453
Evaluate side-chains
  82 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 45 optimal weight:    6.9990
   chunk 8 optimal weight:    7.9990
   chunk 70 optimal weight:   10.0000
   chunk 41 optimal weight:    5.9990
   chunk 26 optimal weight:   30.0000
   chunk 73 optimal weight:   10.0000
   chunk 0 optimal weight:   30.0000
   chunk 5 optimal weight:    5.9990
   chunk 11 optimal weight:    7.9990
   chunk 18 optimal weight:    5.9990
   chunk 69 optimal weight:    6.9990
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  81 ASN
E  85 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.041617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.033230 restraints weight = 157377.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.034822 restraints weight = 94547.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.035978 restraints weight = 64217.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.036819 restraints weight = 46647.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.037480 restraints weight = 35722.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.6811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.063  12724  Z= 0.276
  Angle     :  0.762  12.860  18454  Z= 0.450
  Chirality :  0.043   0.174   2110
  Planarity :  0.006   0.066   1313
  Dihedral  : 33.995 178.302   4038
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 26.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  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 (0.30), residues: 728
  helix:  1.08 (0.22), residues: 514
  sheet:  None (None), residues: 0
  loop : -1.94 (0.38), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG G  42 
 TYR   0.031   0.003   TYR B  72 
 PHE   0.037   0.003   PHE A 104 
 HIS   0.006   0.001   HIS C  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00588 (12724)
  covalent geometry    : angle       0.76208 (18454)
  hydrogen bonds       : bond        0.09708 (  774)
  hydrogen bonds       : angle       4.29771 ( 1921)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1666.21 seconds
wall clock time: 29 minutes 46.98 seconds (1786.98 seconds total)