Starting phenix.real_space_refine
on Sat Nov 16 21:32:02 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jl9_36389/11_2024/8jl9_36389.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jl9_36389/11_2024/8jl9_36389.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jl9_36389/11_2024/8jl9_36389.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jl9_36389/11_2024/8jl9_36389.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jl9_36389/11_2024/8jl9_36389.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jl9_36389/11_2024/8jl9_36389.cif"
  }
  resolution = 2.65
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.033
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     310      5.49       5
     S      14      5.16       5
     C    6763      2.51       5
     N    2312      2.21       5
     O    2915      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 12314
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 790
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 627
          Classifications: {'peptide': 79}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "C"
      Number of atoms: 831
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 831
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 735
          Classifications: {'peptide': 94}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "E"
      Number of atoms: 783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 783
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
    Chain: "F"
      Number of atoms: 627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 627
          Classifications: {'peptide': 79}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "G"
      Number of atoms: 831
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 831
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "H"
      Number of atoms: 735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 735
          Classifications: {'peptide': 94}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "I"
      Number of atoms: 3178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 155, 3178
          Classifications: {'DNA': 155}
          Link IDs: {'rna3p': 154}
    Chain: "J"
      Number of atoms: 3177
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 155, 3177
          Classifications: {'DNA': 155}
          Link IDs: {'rna3p': 154}
  Time building chain proxies: 7.72, per 1000 atoms: 0.63
  Number of scatterers: 12314
  At special positions: 0
  Unit cell: (74.2, 120.84, 129.32, 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      14     16.00
     P     310     15.00
     O    2915      8.00
     N    2312      7.00
     C    6763      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: 3.13
  Conformation dependent library (CDL) restraints added in 981.7 milliseconds
  

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1398

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 10 sheets defined
      73.4% alpha, 3.2% beta
      155 base pairs and 283 stacking pairs defined.
    Time for finding SS restraints: 6.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 3.932A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.656A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.481A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
      removed outlier: 3.504A  pdb=" N   LEU C 116 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 104 through 123
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 3.973A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 24 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.671A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 36
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.474A  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 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 104 through 123
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.897A  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
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.277A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (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 100 through 102
      removed outlier: 6.329A  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: 6.914A  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
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.126A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (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

    412 hydrogen bonds defined for protein.
    1212 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      398 hydrogen bonds
      796 hydrogen bond angles
      0 basepair planarities
      155 basepair parallelities
      283 stacking parallelities
  Total time for adding SS restraints: 4.91

  Time building geometry restraints manager: 3.66 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: 2146
        1.33 -     1.45: 4427
        1.45 -     1.57: 5950
        1.57 -     1.69: 619
        1.69 -     1.81: 24
  Bond restraints: 13166
  Sorted by residual:
  bond pdb=" C   SER D  32 "
       pdb=" N   ARG D  33 "
    ideal  model  delta    sigma   weight residual
    1.330  1.257  0.073 1.39e-02 5.18e+03 2.73e+01
  bond pdb=" CZ  ARG E 131 "
       pdb=" NH2 ARG E 131 "
    ideal  model  delta    sigma   weight residual
    1.330  1.285  0.045 1.30e-02 5.92e+03 1.22e+01
  bond pdb=" CZ  ARG G  88 "
       pdb=" NH2 ARG G  88 "
    ideal  model  delta    sigma   weight residual
    1.330  1.288  0.042 1.30e-02 5.92e+03 1.02e+01
  bond pdb=" CZ  ARG E 116 "
       pdb=" NH2 ARG E 116 "
    ideal  model  delta    sigma   weight residual
    1.330  1.290  0.040 1.30e-02 5.92e+03 9.45e+00
  bond pdb=" CZ  ARG D  72 "
       pdb=" NH2 ARG D  72 "
    ideal  model  delta    sigma   weight residual
    1.330  1.290  0.040 1.30e-02 5.92e+03 9.27e+00
  ... (remaining 13161 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.25: 18407
        2.25 -     4.50: 671
        4.50 -     6.75: 33
        6.75 -     9.00: 0
        9.00 -    11.25: 1
  Bond angle restraints: 19112
  Sorted by residual:
  angle pdb=" C   SER D  32 "
        pdb=" CA  SER D  32 "
        pdb=" CB  SER D  32 "
      ideal   model   delta    sigma   weight residual
     110.42  121.67  -11.25 1.99e+00 2.53e-01 3.20e+01
  angle pdb=" O   SER D  32 "
        pdb=" C   SER D  32 "
        pdb=" N   ARG D  33 "
      ideal   model   delta    sigma   weight residual
     122.59  116.13    6.46 1.33e+00 5.65e-01 2.36e+01
  angle pdb=" CA  PRO A  38 "
        pdb=" N   PRO A  38 "
        pdb=" CD  PRO A  38 "
      ideal   model   delta    sigma   weight residual
     112.00  106.41    5.59 1.40e+00 5.10e-01 1.60e+01
  angle pdb=" CA  ILE H  61 "
        pdb=" CB  ILE H  61 "
        pdb=" CG1 ILE H  61 "
      ideal   model   delta    sigma   weight residual
     110.40  117.02   -6.62 1.70e+00 3.46e-01 1.52e+01
  angle pdb=" CD  ARG E 131 "
        pdb=" NE  ARG E 131 "
        pdb=" CZ  ARG E 131 "
      ideal   model   delta    sigma   weight residual
     124.40  129.82   -5.42 1.40e+00 5.10e-01 1.50e+01
  ... (remaining 19107 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.16: 5357
       32.16 -    64.31: 1688
       64.31 -    96.47: 53
       96.47 -   128.63: 0
      128.63 -   160.79: 2
  Dihedral angle restraints: 7100
    sinusoidal: 4927
      harmonic: 2173
  Sorted by residual:
  dihedral pdb=" C   SER D  32 "
           pdb=" N   SER D  32 "
           pdb=" CA  SER D  32 "
           pdb=" CB  SER D  32 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -140.37   17.77     0      2.50e+00 1.60e-01 5.05e+01
  dihedral pdb=" N   SER D  32 "
           pdb=" C   SER D  32 "
           pdb=" CA  SER D  32 "
           pdb=" CB  SER D  32 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  135.82  -13.02     0      2.50e+00 1.60e-01 2.71e+01
  dihedral pdb=" CA  ARG D  33 "
           pdb=" C   ARG D  33 "
           pdb=" N   LYS D  34 "
           pdb=" CA  LYS D  34 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.72   20.28     0      5.00e+00 4.00e-02 1.64e+01
  ... (remaining 7097 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.119: 2123
       0.119 -    0.238: 41
       0.238 -    0.357: 6
       0.357 -    0.476: 0
       0.476 -    0.595: 1
  Chirality restraints: 2171
  Sorted by residual:
  chirality pdb=" CA  SER D  32 "
            pdb=" N   SER D  32 "
            pdb=" C   SER D  32 "
            pdb=" CB  SER D  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.92    0.60 2.00e-01 2.50e+01 8.86e+00
  chirality pdb=" CA  PRO B  32 "
            pdb=" N   PRO B  32 "
            pdb=" C   PRO B  32 "
            pdb=" CB  PRO B  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.39    0.32 2.00e-01 2.50e+01 2.62e+00
  chirality pdb=" CA  PRO F  32 "
            pdb=" N   PRO F  32 "
            pdb=" C   PRO F  32 "
            pdb=" CB  PRO F  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.40    0.31 2.00e-01 2.50e+01 2.46e+00
  ... (remaining 2168 not shown)

  Planarity restraints: 1347
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D  40 "   -0.099 2.00e-02 2.50e+03   5.09e-02 5.18e+01
        pdb=" CG  TYR D  40 "    0.052 2.00e-02 2.50e+03
        pdb=" CD1 TYR D  40 "    0.033 2.00e-02 2.50e+03
        pdb=" CD2 TYR D  40 "    0.057 2.00e-02 2.50e+03
        pdb=" CE1 TYR D  40 "    0.023 2.00e-02 2.50e+03
        pdb=" CE2 TYR D  40 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR D  40 "   -0.011 2.00e-02 2.50e+03
        pdb=" OH  TYR D  40 "   -0.056 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG G  17 "   -0.531 9.50e-02 1.11e+02   2.38e-01 3.48e+01
        pdb=" NE  ARG G  17 "    0.032 2.00e-02 2.50e+03
        pdb=" CZ  ARG G  17 "    0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG G  17 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG G  17 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT I -76 "    0.052 2.00e-02 2.50e+03   2.80e-02 1.96e+01
        pdb=" N1   DT I -76 "   -0.070 2.00e-02 2.50e+03
        pdb=" C2   DT I -76 "    0.002 2.00e-02 2.50e+03
        pdb=" O2   DT I -76 "   -0.004 2.00e-02 2.50e+03
        pdb=" N3   DT I -76 "    0.004 2.00e-02 2.50e+03
        pdb=" C4   DT I -76 "    0.008 2.00e-02 2.50e+03
        pdb=" O4   DT I -76 "    0.012 2.00e-02 2.50e+03
        pdb=" C5   DT I -76 "   -0.000 2.00e-02 2.50e+03
        pdb=" C7   DT I -76 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DT I -76 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 1344 not shown)

  Histogram of nonbonded interaction distances:
        1.87 -     2.47: 8
        2.47 -     3.08: 7511
        3.08 -     3.69: 20503
        3.69 -     4.29: 32533
        4.29 -     4.90: 46271
  Nonbonded interactions: 106826
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP F  68 "
            pdb=" NH1 ARG F  92 "
     model   vdw
     1.865 3.120
  nonbonded pdb=" NH2 ARG F  92 "
            pdb=" O   LEU H 100 "
     model   vdw
     2.337 3.120
  nonbonded pdb=" O   HIS F  75 "
            pdb=" NH1 ARG H  92 "
     model   vdw
     2.399 3.120
  nonbonded pdb=" OH  TYR E  99 "
            pdb=" OE1 GLU E 133 "
     model   vdw
     2.403 3.040
  nonbonded pdb=" O   ASN D  67 "
            pdb=" OE1 GLU D  71 "
     model   vdw
     2.403 3.040
  ... (remaining 106821 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 39 through 133)
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}
ncs_group {
  reference = (chain 'I' and (resid -77 through -1 or resid 1 through 77))
  selection = (chain 'J' and (resid -77 through -1 or resid 1 through 77))
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.460
  Check model and map are aligned:         0.080
  Set scattering table:                    0.150
  Process input model:                     34.150
  Find NCS groups from input model:        0.370
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   49.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6287
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      :  0.005   0.111  13166  Z= 0.322
  Angle     :  0.857  11.254  19112  Z= 0.565
  Chirality :  0.048   0.595   2171
  Planarity :  0.012   0.238   1347
  Dihedral  : 28.861 160.785   5702
  Min Nonbonded Distance : 1.865

Molprobity Statistics.
  All-atom Clashscore : 2.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 13.16 %
    Favored  : 86.84 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.27), residues: 737
  helix:  0.48 (0.20), residues: 532
  sheet:  None (None), residues: 0
  loop : -0.40 (0.37), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS H 109 
 PHE   0.012   0.002   PHE A  84 
 TYR   0.099   0.004   TYR D  40 
 ARG   0.005   0.001   ARG A  63 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.868 
Fit side-chains
REVERT: A   60 LEU cc_start: 0.7253 (mt) cc_final: 0.7029 (mt)
REVERT: A  106 ASP cc_start: 0.6034 (m-30) cc_final: 0.5524 (m-30)
REVERT: A  120 MET cc_start: 0.6701 (mtt) cc_final: 0.6388 (mtm)
REVERT: A  123 ASP cc_start: 0.6922 (m-30) cc_final: 0.6526 (m-30)
REVERT: A  128 ARG cc_start: 0.6531 (mtp180) cc_final: 0.6273 (mmm160)
REVERT: B   79 LYS cc_start: 0.6802 (mmtm) cc_final: 0.6554 (mmtp)
REVERT: B   84 MET cc_start: 0.6224 (mmm) cc_final: 0.5991 (mmp)
REVERT: C  104 GLN cc_start: 0.7350 (tp40) cc_final: 0.6913 (mp10)
REVERT: E   53 ARG cc_start: 0.6337 (ttp-110) cc_final: 0.5974 (ttp-110)
REVERT: E  120 MET cc_start: 0.6824 (mtt) cc_final: 0.6491 (mtm)
REVERT: E  122 LYS cc_start: 0.6425 (pttt) cc_final: 0.6153 (pttp)
REVERT: G   40 SER cc_start: 0.7793 (p) cc_final: 0.7524 (p)
REVERT: G   42 ARG cc_start: 0.5862 (mtp85) cc_final: 0.5392 (mtp85)
REVERT: G   89 ASN cc_start: 0.7383 (m-40) cc_final: 0.6977 (m110)
REVERT: H   71 GLU cc_start: 0.6421 (pt0) cc_final: 0.6035 (pt0)
REVERT: H  108 LYS cc_start: 0.7308 (tttp) cc_final: 0.7021 (ttpp)
  outliers start: 0
  outliers final: 1
  residues processed: 146
  average time/residue: 2.0574
  time to fit residues: 316.0155
Evaluate side-chains
  128 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 127
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  101 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 51 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   chunk 78 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 58 optimal weight:    0.6980
   chunk 90 optimal weight:    2.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
A  68 GLN
A 125 GLN
F  25 ASN
F  27 GLN
F  93 GLN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  84 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6336
moved from start:          0.1871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13166  Z= 0.234
  Angle     :  0.571   5.029  19112  Z= 0.355
  Chirality :  0.036   0.134   2171
  Planarity :  0.004   0.036   1347
  Dihedral  : 30.304 170.437   4225
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 17.66 %
    Favored  : 80.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.82 (0.30), residues: 737
  helix:  2.60 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.30 (0.38), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 113 
 PHE   0.006   0.001   PHE E  67 
 TYR   0.012   0.001   TYR H  40 
 ARG   0.005   0.000   ARG C  71 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 119
  time to evaluate  : 0.956 
Fit side-chains
REVERT: A   40 ARG cc_start: 0.7155 (mtp-110) cc_final: 0.6551 (mtt-85)
REVERT: A   56 LYS cc_start: 0.7300 (ttpp) cc_final: 0.7038 (ttmm)
REVERT: A   83 ARG cc_start: 0.6922 (OUTLIER) cc_final: 0.4876 (mtm180)
REVERT: A  106 ASP cc_start: 0.6010 (m-30) cc_final: 0.5623 (m-30)
REVERT: A  128 ARG cc_start: 0.6493 (mtp180) cc_final: 0.6207 (mmm160)
REVERT: B   84 MET cc_start: 0.6251 (mmm) cc_final: 0.5942 (mmp)
REVERT: C  104 GLN cc_start: 0.7514 (tp40) cc_final: 0.6733 (mp10)
REVERT: D   71 GLU cc_start: 0.6182 (OUTLIER) cc_final: 0.5701 (mt-10)
REVERT: E  120 MET cc_start: 0.6085 (mtt) cc_final: 0.5820 (mtm)
REVERT: F   84 MET cc_start: 0.6395 (mmm) cc_final: 0.5964 (mmm)
REVERT: G   73 ASN cc_start: 0.6096 (t0) cc_final: 0.5852 (t160)
REVERT: H   78 SER cc_start: 0.7157 (t) cc_final: 0.6848 (p)
  outliers start: 9
  outliers final: 1
  residues processed: 120
  average time/residue: 2.1173
  time to fit residues: 267.2732
Evaluate side-chains
  109 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 106
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 ARG
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain H residue   87 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   chunk 75 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 90 optimal weight:    2.9990
   chunk 98 optimal weight:    3.9990
   chunk 81 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 72 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
C  73 ASN
E  68 GLN
F  25 ASN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6389
moved from start:          0.2704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.044  13166  Z= 0.413
  Angle     :  0.646   5.170  19112  Z= 0.394
  Chirality :  0.043   0.149   2171
  Planarity :  0.005   0.047   1347
  Dihedral  : 30.327 172.365   4223
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 17.98 %
    Favored  : 78.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.51 (0.30), residues: 737
  helix:  2.37 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.39 (0.38), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.001   HIS A 113 
 PHE   0.010   0.002   PHE H  70 
 TYR   0.019   0.002   TYR D  40 
 ARG   0.005   0.001   ARG C  71 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.923 
Fit side-chains
REVERT: A   40 ARG cc_start: 0.6992 (mtp-110) cc_final: 0.6679 (mtp85)
REVERT: A   42 ARG cc_start: 0.6550 (mtt90) cc_final: 0.6341 (mtt90)
REVERT: A   83 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.5213 (mtm180)
REVERT: A  123 ASP cc_start: 0.6943 (m-30) cc_final: 0.6520 (m-30)
REVERT: B   95 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.6238 (mtp-110)
REVERT: C  104 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.6694 (mp10)
REVERT: D   71 GLU cc_start: 0.6340 (OUTLIER) cc_final: 0.5567 (mp0)
REVERT: E   53 ARG cc_start: 0.6266 (OUTLIER) cc_final: 0.5735 (ttt-90)
REVERT: E  120 MET cc_start: 0.6376 (mtt) cc_final: 0.6044 (mtm)
REVERT: G   73 ASN cc_start: 0.6554 (t0) cc_final: 0.6333 (t160)
REVERT: G   89 ASN cc_start: 0.7347 (m110) cc_final: 0.7033 (m-40)
REVERT: G   91 GLU cc_start: 0.3862 (OUTLIER) cc_final: 0.2961 (tp30)
  outliers start: 20
  outliers final: 4
  residues processed: 106
  average time/residue: 2.4022
  time to fit residues: 266.4781
Evaluate side-chains
  104 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 ARG
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue  104 GLN
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain D residue   91 SER
Chi-restraints excluded: chain E residue   53 ARG
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue   87 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 68 optimal weight:    0.9980
   chunk 47 optimal weight:    0.6980
   chunk 10 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 91 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 86 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 80 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  63 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6373
moved from start:          0.2698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13166  Z= 0.224
  Angle     :  0.590   5.006  19112  Z= 0.369
  Chirality :  0.038   0.127   2171
  Planarity :  0.004   0.048   1347
  Dihedral  : 30.349 173.148   4223
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 19.26 %
    Favored  : 78.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.78 (0.30), residues: 737
  helix:  2.57 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.30 (0.38), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  75 
 PHE   0.016   0.001   PHE D  70 
 TYR   0.012   0.001   TYR D  40 
 ARG   0.003   0.000   ARG C  71 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.936 
Fit side-chains
REVERT: A   40 ARG cc_start: 0.6966 (mtp-110) cc_final: 0.6356 (mtt-85)
REVERT: A   42 ARG cc_start: 0.6533 (mtt90) cc_final: 0.6090 (mtt90)
REVERT: A  123 ASP cc_start: 0.6887 (m-30) cc_final: 0.6491 (m-30)
REVERT: B   84 MET cc_start: 0.6143 (mmm) cc_final: 0.5874 (mmp)
REVERT: B   95 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6352 (mtt-85)
REVERT: C  104 GLN cc_start: 0.7456 (OUTLIER) cc_final: 0.6665 (mp10)
REVERT: D   71 GLU cc_start: 0.6154 (OUTLIER) cc_final: 0.5390 (mp0)
REVERT: E  120 MET cc_start: 0.6229 (mtt) cc_final: 0.5931 (mtm)
REVERT: G   73 ASN cc_start: 0.6531 (t0) cc_final: 0.6300 (t160)
REVERT: G   89 ASN cc_start: 0.7332 (m110) cc_final: 0.6996 (m-40)
REVERT: G   91 GLU cc_start: 0.3747 (OUTLIER) cc_final: 0.2930 (tp30)
  outliers start: 12
  outliers final: 3
  residues processed: 100
  average time/residue: 2.4664
  time to fit residues: 257.8051
Evaluate side-chains
  93 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue  104 GLN
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue   91 SER
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue   71 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 71 optimal weight:    3.9990
   chunk 39 optimal weight:    0.3980
   chunk 82 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0270
   chunk 0 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 86 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 87 optimal weight:    2.9990
   overall best weight:    0.5840

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
B  93 GLN
F  25 ASN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  63 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6360
moved from start:          0.2682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13166  Z= 0.205
  Angle     :  0.571   9.145  19112  Z= 0.354
  Chirality :  0.036   0.123   2171
  Planarity :  0.005   0.056   1347
  Dihedral  : 30.300 172.073   4223
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 20.06 %
    Favored  : 78.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.05 (0.30), residues: 737
  helix:  2.76 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.16 (0.39), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D 109 
 PHE   0.006   0.001   PHE A  67 
 TYR   0.010   0.001   TYR C  50 
 ARG   0.004   0.000   ARG C  71 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.937 
Fit side-chains
REVERT: A   40 ARG cc_start: 0.6982 (mtp-110) cc_final: 0.6465 (mtp85)
REVERT: A   42 ARG cc_start: 0.6502 (mtt90) cc_final: 0.6218 (mtt90)
REVERT: B   84 MET cc_start: 0.6249 (mmm) cc_final: 0.5959 (mmp)
REVERT: B   95 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.6310 (mtt-85)
REVERT: C  104 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.6573 (mp10)
REVERT: D   71 GLU cc_start: 0.6127 (OUTLIER) cc_final: 0.5355 (mp0)
REVERT: E   53 ARG cc_start: 0.6309 (OUTLIER) cc_final: 0.5742 (ttt-90)
REVERT: E  120 MET cc_start: 0.6147 (mtt) cc_final: 0.5787 (mtm)
REVERT: G   73 ASN cc_start: 0.6553 (t0) cc_final: 0.6289 (t160)
REVERT: G   89 ASN cc_start: 0.7288 (m110) cc_final: 0.6935 (m-40)
REVERT: G   91 GLU cc_start: 0.3796 (OUTLIER) cc_final: 0.2992 (tp30)
  outliers start: 12
  outliers final: 4
  residues processed: 103
  average time/residue: 2.4390
  time to fit residues: 262.8133
Evaluate side-chains
  98 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue  104 GLN
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain E residue   53 ARG
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue   71 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 19 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0570
   chunk 8 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 50 optimal weight:    0.7980
   chunk 93 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.6698

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
E  68 GLN
F  25 ASN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  63 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6345
moved from start:          0.2699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13166  Z= 0.205
  Angle     :  0.543   5.077  19112  Z= 0.339
  Chirality :  0.035   0.123   2171
  Planarity :  0.004   0.043   1347
  Dihedral  : 30.182 172.500   4223
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 20.39 %
    Favored  : 77.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.20 (0.30), residues: 737
  helix:  2.86 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.07 (0.40), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS D 109 
 PHE   0.006   0.001   PHE A  67 
 TYR   0.009   0.001   TYR H  40 
 ARG   0.011   0.000   ARG A  83 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 1.000 
Fit side-chains
REVERT: A   40 ARG cc_start: 0.7006 (mtp-110) cc_final: 0.6515 (mtp85)
REVERT: A   42 ARG cc_start: 0.6513 (mtt90) cc_final: 0.6213 (mtt90)
REVERT: A  106 ASP cc_start: 0.6183 (m-30) cc_final: 0.5813 (m-30)
REVERT: B   84 MET cc_start: 0.6259 (mmm) cc_final: 0.5983 (mmp)
REVERT: B   95 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.6202 (mtp-110)
REVERT: C  104 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.6554 (mp10)
REVERT: D   71 GLU cc_start: 0.6311 (OUTLIER) cc_final: 0.5490 (mp0)
REVERT: E  133 GLU cc_start: 0.6503 (OUTLIER) cc_final: 0.5824 (mt-10)
REVERT: G   73 ASN cc_start: 0.6496 (t0) cc_final: 0.6179 (t0)
REVERT: G   89 ASN cc_start: 0.7247 (m110) cc_final: 0.7027 (m-40)
REVERT: G   91 GLU cc_start: 0.3806 (OUTLIER) cc_final: 0.3057 (tp30)
  outliers start: 13
  outliers final: 5
  residues processed: 107
  average time/residue: 2.2681
  time to fit residues: 254.6685
Evaluate side-chains
  106 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue  104 GLN
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain G residue   20 ARG
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue   71 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 70 optimal weight:    7.9990
   chunk 54 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 44 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 57 optimal weight:    0.5980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
B  93 GLN
C  73 ASN
F  25 ASN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  63 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6354
moved from start:          0.2759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13166  Z= 0.229
  Angle     :  0.552   5.289  19112  Z= 0.343
  Chirality :  0.035   0.122   2171
  Planarity :  0.004   0.044   1347
  Dihedral  : 30.155 173.055   4223
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 21.51 %
    Favored  : 76.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.13 (0.30), residues: 737
  helix:  2.80 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.06 (0.40), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D 109 
 PHE   0.005   0.001   PHE H  70 
 TYR   0.010   0.001   TYR D  40 
 ARG   0.006   0.000   ARG A  83 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.809 
Fit side-chains
REVERT: A   40 ARG cc_start: 0.6994 (mtp-110) cc_final: 0.6515 (mtp85)
REVERT: A   42 ARG cc_start: 0.6518 (mtt90) cc_final: 0.6214 (mtt90)
REVERT: A  106 ASP cc_start: 0.6196 (m-30) cc_final: 0.5810 (m-30)
REVERT: A  123 ASP cc_start: 0.6938 (m-30) cc_final: 0.6517 (m-30)
REVERT: B   84 MET cc_start: 0.6263 (mmm) cc_final: 0.5983 (mmp)
REVERT: B   95 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.6357 (mtt-85)
REVERT: C   73 ASN cc_start: 0.6495 (OUTLIER) cc_final: 0.6273 (t0)
REVERT: C  104 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.6556 (mp10)
REVERT: D   71 GLU cc_start: 0.6315 (OUTLIER) cc_final: 0.5498 (mp0)
REVERT: E   53 ARG cc_start: 0.6319 (OUTLIER) cc_final: 0.5740 (ttt-90)
REVERT: E  120 MET cc_start: 0.6137 (mtt) cc_final: 0.5779 (mtm)
REVERT: G   73 ASN cc_start: 0.6491 (t0) cc_final: 0.6186 (t0)
REVERT: G   89 ASN cc_start: 0.7267 (m110) cc_final: 0.7048 (m-40)
REVERT: G   91 GLU cc_start: 0.3823 (OUTLIER) cc_final: 0.3055 (tp30)
  outliers start: 11
  outliers final: 4
  residues processed: 100
  average time/residue: 2.3989
  time to fit residues: 251.7516
Evaluate side-chains
  104 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 1.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   73 ASN
Chi-restraints excluded: chain C residue  104 GLN
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain E residue   53 ARG
Chi-restraints excluded: chain G residue   20 ARG
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue   71 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 47 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   chunk 75 optimal weight:    2.9990
   chunk 87 optimal weight:    3.9990
   chunk 92 optimal weight:    2.9990
   chunk 84 optimal weight:    3.9990
   chunk 89 optimal weight:    2.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
C  73 ASN
F  25 ASN
F  75 HIS
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  63 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6357
moved from start:          0.2830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13166  Z= 0.240
  Angle     :  0.556   6.392  19112  Z= 0.344
  Chirality :  0.036   0.122   2171
  Planarity :  0.004   0.044   1347
  Dihedral  : 30.152 174.226   4223
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 21.19 %
    Favored  : 76.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.11 (0.30), residues: 737
  helix:  2.78 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.07 (0.40), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 113 
 PHE   0.005   0.001   PHE H  70 
 TYR   0.009   0.001   TYR D  40 
 ARG   0.005   0.000   ARG A  83 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.874 
Fit side-chains
REVERT: A   40 ARG cc_start: 0.6966 (mtp-110) cc_final: 0.6481 (mtp85)
REVERT: A   42 ARG cc_start: 0.6495 (mtt90) cc_final: 0.6203 (mtt90)
REVERT: A  106 ASP cc_start: 0.6220 (m-30) cc_final: 0.5837 (m-30)
REVERT: B   84 MET cc_start: 0.6254 (mmm) cc_final: 0.5977 (mmp)
REVERT: B   95 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.6381 (mtt-85)
REVERT: C  104 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.6555 (mp10)
REVERT: D   71 GLU cc_start: 0.6320 (OUTLIER) cc_final: 0.5509 (mp0)
REVERT: E   53 ARG cc_start: 0.6324 (OUTLIER) cc_final: 0.5773 (ttt-90)
REVERT: E  133 GLU cc_start: 0.6546 (OUTLIER) cc_final: 0.5877 (mt-10)
REVERT: G   73 ASN cc_start: 0.6513 (t0) cc_final: 0.6193 (t0)
REVERT: G   89 ASN cc_start: 0.7275 (m110) cc_final: 0.6963 (m-40)
REVERT: G   91 GLU cc_start: 0.3780 (OUTLIER) cc_final: 0.2984 (tp30)
REVERT: H   79 ARG cc_start: 0.6312 (OUTLIER) cc_final: 0.6076 (mtt90)
  outliers start: 13
  outliers final: 4
  residues processed: 102
  average time/residue: 2.3279
  time to fit residues: 248.5858
Evaluate side-chains
  105 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue  104 GLN
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain E residue   53 ARG
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain G residue   20 ARG
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain H residue   79 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 54 optimal weight:    0.7980
   chunk 39 optimal weight:    0.8980
   chunk 70 optimal weight:    7.9990
   chunk 27 optimal weight:    0.6980
   chunk 81 optimal weight:    2.9990
   chunk 84 optimal weight:    3.9990
   chunk 89 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 94 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
C  73 ASN
F  25 ASN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  63 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6356
moved from start:          0.2833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13166  Z= 0.224
  Angle     :  0.553   6.323  19112  Z= 0.343
  Chirality :  0.035   0.122   2171
  Planarity :  0.004   0.044   1347
  Dihedral  : 30.154 174.238   4223
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 21.51 %
    Favored  : 76.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.14 (0.30), residues: 737
  helix:  2.80 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.06 (0.40), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 113 
 PHE   0.005   0.001   PHE A  67 
 TYR   0.009   0.001   TYR D  40 
 ARG   0.005   0.000   ARG A  83 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.910 
Fit side-chains
REVERT: A   40 ARG cc_start: 0.6965 (mtp-110) cc_final: 0.6487 (mtp85)
REVERT: A   42 ARG cc_start: 0.6494 (mtt90) cc_final: 0.6200 (mtt90)
REVERT: A  106 ASP cc_start: 0.6229 (m-30) cc_final: 0.5834 (m-30)
REVERT: B   84 MET cc_start: 0.6252 (mmm) cc_final: 0.5979 (mmp)
REVERT: B   95 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.6349 (mtt-85)
REVERT: C  104 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.6554 (mp10)
REVERT: D   71 GLU cc_start: 0.6319 (OUTLIER) cc_final: 0.5509 (mp0)
REVERT: E   53 ARG cc_start: 0.6321 (OUTLIER) cc_final: 0.5772 (ttt-90)
REVERT: E  133 GLU cc_start: 0.6549 (OUTLIER) cc_final: 0.5873 (mt-10)
REVERT: G   73 ASN cc_start: 0.6511 (t0) cc_final: 0.6190 (t0)
REVERT: G   89 ASN cc_start: 0.7273 (m110) cc_final: 0.6961 (m-40)
REVERT: G   91 GLU cc_start: 0.3776 (OUTLIER) cc_final: 0.2982 (tp30)
REVERT: H   79 ARG cc_start: 0.6321 (OUTLIER) cc_final: 0.6077 (mtt90)
  outliers start: 13
  outliers final: 4
  residues processed: 101
  average time/residue: 2.3441
  time to fit residues: 247.7657
Evaluate side-chains
  104 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 1.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue  104 GLN
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain E residue   53 ARG
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain G residue   20 ARG
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain H residue   79 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 99 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 48 optimal weight:    0.6980
   chunk 63 optimal weight:    2.9990
   chunk 84 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
D  84 ASN
E  68 GLN
F  25 ASN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  63 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6378
moved from start:          0.2902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041  13166  Z= 0.334
  Angle     :  0.598   6.454  19112  Z= 0.366
  Chirality :  0.040   0.138   2171
  Planarity :  0.005   0.045   1347
  Dihedral  : 30.190 175.148   4223
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 21.99 %
    Favored  : 76.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.86 (0.30), residues: 737
  helix:  2.61 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.19 (0.39), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS A 113 
 PHE   0.007   0.002   PHE C  25 
 TYR   0.016   0.002   TYR D  40 
 ARG   0.005   0.000   ARG E 129 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.936 
Fit side-chains
REVERT: A   40 ARG cc_start: 0.6947 (mtp-110) cc_final: 0.6545 (mtp85)
REVERT: A   42 ARG cc_start: 0.6523 (mtt90) cc_final: 0.6232 (mtt90)
REVERT: A  123 ASP cc_start: 0.6933 (m-30) cc_final: 0.6499 (m-30)
REVERT: B   95 ARG cc_start: 0.7272 (OUTLIER) cc_final: 0.6213 (mtp-110)
REVERT: C  104 GLN cc_start: 0.7398 (OUTLIER) cc_final: 0.6581 (mp10)
REVERT: D   71 GLU cc_start: 0.6316 (OUTLIER) cc_final: 0.5549 (mp0)
REVERT: E   53 ARG cc_start: 0.6337 (OUTLIER) cc_final: 0.6031 (ttt90)
REVERT: E  120 MET cc_start: 0.6225 (mtt) cc_final: 0.5865 (mtm)
REVERT: E  133 GLU cc_start: 0.6504 (OUTLIER) cc_final: 0.5838 (mt-10)
REVERT: G   73 ASN cc_start: 0.6570 (t0) cc_final: 0.6218 (t0)
REVERT: G   89 ASN cc_start: 0.7317 (m110) cc_final: 0.6990 (m-40)
REVERT: G   91 GLU cc_start: 0.3798 (OUTLIER) cc_final: 0.2960 (tp30)
  outliers start: 10
  outliers final: 3
  residues processed: 97
  average time/residue: 2.4724
  time to fit residues: 250.6207
Evaluate side-chains
  101 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue  104 GLN
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain E residue   53 ARG
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue   71 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 81 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9980
   chunk 69 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   chunk 57 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  63 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.112366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.097047 restraints weight = 16175.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.3206 rms_B_bonded: 0.78
r_work: 0.3106 rms_B_bonded: 1.55 restraints_weight: 0.5000
r_work: 0.2999 rms_B_bonded: 2.70 restraints_weight: 0.2500
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.2908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  13166  Z= 0.218
  Angle     :  0.580   6.590  19112  Z= 0.359
  Chirality :  0.036   0.126   2171
  Planarity :  0.004   0.043   1347
  Dihedral  : 30.216 174.797   4223
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 21.99 %
    Favored  : 76.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.95 (0.30), residues: 737
  helix:  2.67 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.16 (0.39), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 113 
 PHE   0.005   0.001   PHE A  67 
 TYR   0.013   0.002   TYR D  40 
 ARG   0.005   0.000   ARG E 129 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4235.08 seconds
wall clock time: 76 minutes 16.50 seconds (4576.50 seconds total)