Starting phenix.real_space_refine
on Wed Mar 12 18:16:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7oz3_13119/03_2025/7oz3_13119.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7oz3_13119/03_2025/7oz3_13119.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.46
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7oz3_13119/03_2025/7oz3_13119.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7oz3_13119/03_2025/7oz3_13119.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7oz3_13119/03_2025/7oz3_13119.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7oz3_13119/03_2025/7oz3_13119.cif"
  }
  resolution = 4.46
  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=   0.000 sd=   0.002
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      92      5.49       5
     S       8      5.16       5
     C    4932      2.51       5
     N    1411      2.21       5
     O    1766      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8209
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1584
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1584
          Classifications: {'peptide': 202}
          Link IDs: {'PTRANS': 5, 'TRANS': 196}
    Chain: "B"
      Number of atoms: 1595
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 203, 1595
          Classifications: {'peptide': 203}
          Link IDs: {'PTRANS': 5, 'TRANS': 197}
    Chain: "C"
      Number of atoms: 1580
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1580
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 5, 'TRANS': 195}
    Chain: "D"
      Number of atoms: 1558
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1558
          Classifications: {'peptide': 198}
          Link IDs: {'PTRANS': 5, 'TRANS': 192}
    Chain: "F"
      Number of atoms: 900
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 900
          Classifications: {'DNA': 44}
          Link IDs: {'rna3p': 43}
    Chain: "G"
      Number of atoms: 904
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 904
          Classifications: {'DNA': 44}
          Link IDs: {'rna3p': 43}
    Chain: "A"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Classifications: {'RNA': 1}
    Chain: "B"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Classifications: {'RNA': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   ARG C 210 " occ=0.75
      ... (9 atoms not shown)
      pdb=" NH2 ARG C 210 " occ=0.75
  Time building chain proxies: 5.61, per 1000 atoms: 0.68
  Number of scatterers: 8209
  At special positions: 0
  Unit cell: (77.404, 93.094, 161.084, 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       8     16.00
     P      92     15.00
     O    1766      8.00
     N    1411      7.00
     C    4932      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: 2.09
  Conformation dependent library (CDL) restraints added in 701.0 milliseconds
  

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1504

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 9 sheets defined
      58.5% alpha, 9.7% beta
      44 base pairs and 82 stacking pairs defined.
    Time for finding SS restraints: 2.90
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 27
    Processing helix  chain 'A' and resid 39 through 46
    Processing helix  chain 'A' and resid 48 through 62
      removed outlier: 3.528A  pdb=" N   LEU A  62 " --> pdb=" O   ILE A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 128
    Processing helix  chain 'A' and resid 129 through 132
    Processing helix  chain 'A' and resid 152 through 157
    Processing helix  chain 'A' and resid 157 through 163
    Processing helix  chain 'A' and resid 196 through 207
    Processing helix  chain 'B' and resid 11 through 27
    Processing helix  chain 'B' and resid 40 through 46
    Processing helix  chain 'B' and resid 48 through 62
      removed outlier: 4.067A  pdb=" N   LEU B  62 " --> pdb=" O   ILE B  58 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 128
      removed outlier: 3.603A  pdb=" N   PHE B 122 " --> pdb=" O   LEU B 118 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   LEU B 123 " --> pdb=" O   VAL B 119 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   LEU B 124 " --> pdb=" O   ASP B 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 132
    Processing helix  chain 'B' and resid 152 through 157
    Processing helix  chain 'B' and resid 157 through 163
    Processing helix  chain 'B' and resid 196 through 207
    Processing helix  chain 'C' and resid 11 through 27
      removed outlier: 4.157A  pdb=" N   ILE C  16 " --> pdb=" O   LYS C  12 " (cutoff:3.500A)
      removed outlier: 5.115A  pdb=" N   ALA C  17 " --> pdb=" O   TYR C  13 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 37 through 46
    Processing helix  chain 'C' and resid 48 through 62
    Processing helix  chain 'C' and resid 77 through 92
      removed outlier: 4.144A  pdb=" N   ALA C  81 " --> pdb=" O   SER C  77 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 94 through 127
      removed outlier: 3.712A  pdb=" N   ARG C 127 " --> pdb=" O   LEU C 123 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 153 through 157
    Processing helix  chain 'C' and resid 157 through 163
    Processing helix  chain 'C' and resid 196 through 208
    Processing helix  chain 'D' and resid 14 through 26
    Processing helix  chain 'D' and resid 37 through 45
    Processing helix  chain 'D' and resid 48 through 62
    Processing helix  chain 'D' and resid 78 through 92
    Processing helix  chain 'D' and resid 94 through 126
    Processing helix  chain 'D' and resid 132 through 136
    Processing helix  chain 'D' and resid 153 through 157
    Processing helix  chain 'D' and resid 157 through 163
    Processing helix  chain 'D' and resid 196 through 207
    Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 35
      removed outlier: 3.637A  pdb=" N   GLY A  72 " --> pdb=" O   LYS A  68 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 141
      removed outlier: 3.500A  pdb=" N   PHE A 193 " --> pdb=" O   TYR A 138 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   VAL A 194 " --> pdb=" O   ILE A 166 " (cutoff:3.500A)
      removed outlier: 5.682A  pdb=" N   ILE A 166 " --> pdb=" O   VAL A 194 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ILE A 169 " --> pdb=" O   ILE A 176 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 34 through 35
    Processing sheet with id=AA4, first strand: chain 'B' and resid 140 through 141
      removed outlier: 6.586A  pdb=" N   VAL B 194 " --> pdb=" O   ILE B 166 " (cutoff:3.500A)
      removed outlier: 5.682A  pdb=" N   ILE B 166 " --> pdb=" O   VAL B 194 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ILE B 169 " --> pdb=" O   ILE B 176 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 65 through 66
      removed outlier: 3.610A  pdb=" N   ILE C  74 " --> pdb=" O   THR C  66 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 138 through 141
      removed outlier: 3.656A  pdb=" N   HIS C 190 " --> pdb=" O   GLU C 170 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   VAL C 194 " --> pdb=" O   ILE C 166 " (cutoff:3.500A)
      removed outlier: 5.682A  pdb=" N   ILE C 166 " --> pdb=" O   VAL C 194 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 151 through 152
      removed outlier: 4.587A  pdb=" N   LYS C 151 " --> pdb=" O   ILE C 185 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 138 through 141
      removed outlier: 6.462A  pdb=" N   VAL D 194 " --> pdb=" O   ILE D 166 " (cutoff:3.500A)
      removed outlier: 5.682A  pdb=" N   ILE D 166 " --> pdb=" O   VAL D 194 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   HIS D 171 " --> pdb=" O   LYS D 174 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 151 through 152
      removed outlier: 4.588A  pdb=" N   LYS D 151 " --> pdb=" O   ILE D 185 " (cutoff:3.500A)

    383 hydrogen bonds defined for protein.
    1104 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      103 hydrogen bonds
      206 hydrogen bond angles
      0 basepair planarities
      44 basepair parallelities
      82 stacking parallelities
  Total time for adding SS restraints: 2.63

  Time building geometry restraints manager: 2.44 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: 1578
        1.33 -     1.45: 2406
        1.45 -     1.57: 4362
        1.57 -     1.69: 185
        1.69 -     1.81: 16
  Bond restraints: 8547
  Sorted by residual:
  bond pdb=" C1' 2BA A 301 "
       pdb=" C2' 2BA A 301 "
    ideal  model  delta    sigma   weight residual
    1.541  1.347  0.194 2.00e-02 2.50e+03 9.38e+01
  bond pdb=" C1' 2BA B 301 "
       pdb=" C2' 2BA B 301 "
    ideal  model  delta    sigma   weight residual
    1.541  1.347  0.194 2.00e-02 2.50e+03 9.38e+01
  bond pdb="C1'1 2BA A 301 "
       pdb="C2'1 2BA A 301 "
    ideal  model  delta    sigma   weight residual
    1.532  1.349  0.183 2.00e-02 2.50e+03 8.41e+01
  bond pdb="C1'1 2BA B 301 "
       pdb="C2'1 2BA B 301 "
    ideal  model  delta    sigma   weight residual
    1.532  1.349  0.183 2.00e-02 2.50e+03 8.38e+01
  bond pdb="C1'1 2BA B 301 "
       pdb="O4'1 2BA B 301 "
    ideal  model  delta    sigma   weight residual
    1.408  1.573 -0.165 2.00e-02 2.50e+03 6.84e+01
  ... (remaining 8542 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.27: 10904
        2.27 -     4.54: 896
        4.54 -     6.82: 145
        6.82 -     9.09: 9
        9.09 -    11.36: 1
  Bond angle restraints: 11955
  Sorted by residual:
  angle pdb=" O3'  DA F  22 "
        pdb=" C3'  DA F  22 "
        pdb=" C2'  DA F  22 "
      ideal   model   delta    sigma   weight residual
     111.50  122.86  -11.36 1.50e+00 4.44e-01 5.74e+01
  angle pdb=" N   SER C 143 "
        pdb=" CA  SER C 143 "
        pdb=" C   SER C 143 "
      ideal   model   delta    sigma   weight residual
     111.69  103.91    7.78 1.23e+00 6.61e-01 4.00e+01
  angle pdb=" N   GLU D 147 "
        pdb=" CA  GLU D 147 "
        pdb=" C   GLU D 147 "
      ideal   model   delta    sigma   weight residual
     112.54  105.73    6.81 1.22e+00 6.72e-01 3.11e+01
  angle pdb=" N   GLU C 147 "
        pdb=" CA  GLU C 147 "
        pdb=" C   GLU C 147 "
      ideal   model   delta    sigma   weight residual
     112.54  105.75    6.79 1.22e+00 6.72e-01 3.09e+01
  angle pdb=" N   ILE B  41 "
        pdb=" CA  ILE B  41 "
        pdb=" C   ILE B  41 "
      ideal   model   delta    sigma   weight residual
     111.44  104.21    7.23 1.34e+00 5.57e-01 2.91e+01
  ... (remaining 11950 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.97: 3890
       19.97 -    39.94: 707
       39.94 -    59.91: 384
       59.91 -    79.88: 8
       79.88 -    99.85: 4
  Dihedral angle restraints: 4993
    sinusoidal: 2661
      harmonic: 2332
  Sorted by residual:
  dihedral pdb=" C   PHE A 207 "
           pdb=" N   PHE A 207 "
           pdb=" CA  PHE A 207 "
           pdb=" CB  PHE A 207 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.85   11.25     0      2.50e+00 1.60e-01 2.03e+01
  dihedral pdb=" C   PHE B 207 "
           pdb=" N   PHE B 207 "
           pdb=" CA  PHE B 207 "
           pdb=" CB  PHE B 207 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.83   11.23     0      2.50e+00 1.60e-01 2.02e+01
  dihedral pdb=" CA  ASN A 157 "
           pdb=" C   ASN A 157 "
           pdb=" N   VAL A 158 "
           pdb=" CA  VAL A 158 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.66  -18.34     0      5.00e+00 4.00e-02 1.35e+01
  ... (remaining 4990 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 1006
       0.082 -    0.165: 288
       0.165 -    0.247: 63
       0.247 -    0.329: 9
       0.329 -    0.411: 5
  Chirality restraints: 1371
  Sorted by residual:
  chirality pdb=" C2' 2BA A 301 "
            pdb=" C1' 2BA A 301 "
            pdb=" C3' 2BA A 301 "
            pdb=" O2' 2BA A 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.80   -2.39   -0.41 2.00e-01 2.50e+01 4.23e+00
  chirality pdb=" C2' 2BA B 301 "
            pdb=" C1' 2BA B 301 "
            pdb=" C3' 2BA B 301 "
            pdb=" O2' 2BA B 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.80   -2.40   -0.41 2.00e-01 2.50e+01 4.10e+00
  chirality pdb=" CA  PHE A 207 "
            pdb=" N   PHE A 207 "
            pdb=" C   PHE A 207 "
            pdb=" CB  PHE A 207 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.08e+00
  ... (remaining 1368 not shown)

  Planarity restraints: 1203
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B  64 "   -0.016 2.00e-02 2.50e+03   3.21e-02 1.03e+01
        pdb=" C   ILE B  64 "    0.056 2.00e-02 2.50e+03
        pdb=" O   ILE B  64 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   LEU B  65 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A  70 "    0.015 2.00e-02 2.50e+03   2.98e-02 8.91e+00
        pdb=" C   GLY A  70 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   GLY A  70 "    0.019 2.00e-02 2.50e+03
        pdb=" N   SER A  71 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT F  19 "    0.001 2.00e-02 2.50e+03   1.84e-02 8.49e+00
        pdb=" N1   DT F  19 "    0.022 2.00e-02 2.50e+03
        pdb=" C2   DT F  19 "   -0.004 2.00e-02 2.50e+03
        pdb=" O2   DT F  19 "   -0.030 2.00e-02 2.50e+03
        pdb=" N3   DT F  19 "    0.006 2.00e-02 2.50e+03
        pdb=" C4   DT F  19 "    0.005 2.00e-02 2.50e+03
        pdb=" O4   DT F  19 "    0.015 2.00e-02 2.50e+03
        pdb=" C5   DT F  19 "    0.006 2.00e-02 2.50e+03
        pdb=" C7   DT F  19 "   -0.037 2.00e-02 2.50e+03
        pdb=" C6   DT F  19 "    0.016 2.00e-02 2.50e+03
  ... (remaining 1200 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.85: 2675
        2.85 -     3.36: 7752
        3.36 -     3.87: 14924
        3.87 -     4.39: 16813
        4.39 -     4.90: 25946
  Nonbonded interactions: 68110
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A  98 "
            pdb=" OD1 ASP B 120 "
     model   vdw
     2.334 3.120
  nonbonded pdb=" OD1 ASP B  28 "
            pdb=" N   TYR B  29 "
     model   vdw
     2.334 3.120
  nonbonded pdb=" O   ALA D 107 "
            pdb=" OE1 GLU D 111 "
     model   vdw
     2.381 3.040
  nonbonded pdb=" O   LEU A  85 "
            pdb=" OE1 GLU A  89 "
     model   vdw
     2.407 3.040
  nonbonded pdb=" O   LEU C 123 "
            pdb=" OG1 THR C 126 "
     model   vdw
     2.432 3.040
  ... (remaining 68105 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 13 through 209)
  selection = (chain 'B' and resid 13 through 209)
  selection = (chain 'C' and resid 13 through 209)
  selection = (chain 'D' and resid 13 through 209)
}

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=0.75 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.330
  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:          0.340
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     23.390
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
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      :  0.011   0.194   8547  Z= 0.620
  Angle     :  1.273  11.360  11955  Z= 0.870
  Chirality :  0.079   0.411   1371
  Planarity :  0.005   0.038   1203
  Dihedral  : 23.029  99.849   3489
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  3.80 %
    Favored  : 95.91 %
  Cbeta Deviations :  0.27 %
  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:  0.64 (0.30), residues: 796
  helix:  1.86 (0.24), residues: 431
  sheet: -1.60 (0.54), residues: 72
  loop : -1.23 (0.37), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.005   TRP B 159 
 HIS   0.004   0.001   HIS C 148 
 PHE   0.019   0.002   PHE A 122 
 TYR   0.025   0.002   TYR A 206 
 ARG   0.008   0.001   ARG A 127 

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 182
  time to evaluate  : 0.881 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8328 (tp30) cc_final: 0.7813 (tp30)
REVERT: A  189 ASP cc_start: 0.8403 (m-30) cc_final: 0.7805 (m-30)
REVERT: A  207 PHE cc_start: 0.8466 (m-80) cc_final: 0.7293 (m-10)
REVERT: B  110 GLN cc_start: 0.8990 (mt0) cc_final: 0.8499 (mp10)
REVERT: B  121 ASP cc_start: 0.9039 (t70) cc_final: 0.8564 (t70)
REVERT: B  133 TYR cc_start: 0.8332 (p90) cc_final: 0.7764 (p90)
REVERT: B  189 ASP cc_start: 0.7421 (m-30) cc_final: 0.7178 (m-30)
REVERT: B  191 ILE cc_start: 0.9263 (mt) cc_final: 0.8893 (mt)
REVERT: C  190 HIS cc_start: 0.8223 (m-70) cc_final: 0.7519 (m170)
REVERT: D   26 ASN cc_start: 0.9392 (t0) cc_final: 0.8860 (t0)
REVERT: D   28 ASP cc_start: 0.8251 (m-30) cc_final: 0.7360 (m-30)
REVERT: D  142 VAL cc_start: 0.8832 (m) cc_final: 0.8517 (p)
  outliers start: 2
  outliers final: 0
  residues processed: 184
  average time/residue: 0.2173
  time to fit residues: 53.0682
Evaluate side-chains
  83 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 73 optimal weight:   10.0000
   chunk 65 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   chunk 35 optimal weight:    4.9990
   chunk 68 optimal weight:    0.2980
   chunk 26 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 79 optimal weight:    3.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 109 GLN
A 125 GLN
B 161 GLN
B 171 HIS
C  57 ASN
C  69 HIS
C  92 HIS
D 161 GLN
D 171 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.065012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.052463 restraints weight = 35959.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.054023 restraints weight = 20499.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.055115 restraints weight = 13698.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2985
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2985 r_free = 0.2985    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2986 r_free = 0.2986    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2986
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.2440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8547  Z= 0.222
  Angle     :  0.621   6.932  11955  Z= 0.367
  Chirality :  0.041   0.270   1371
  Planarity :  0.004   0.050   1203
  Dihedral  : 24.647  97.597   1969
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  5.12 %
    Favored  : 94.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.94 (0.30), residues: 796
  helix:  2.06 (0.24), residues: 438
  sheet: -1.19 (0.55), residues: 68
  loop : -1.19 (0.37), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C 159 
 HIS   0.017   0.001   HIS A 171 
 PHE   0.023   0.002   PHE C 207 
 TYR   0.018   0.002   TYR D 200 
 ARG   0.006   0.001   ARG A  38 

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 120
  time to evaluate  : 1.048 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 MET cc_start: 0.9239 (tpt) cc_final: 0.8892 (tpp)
REVERT: A  207 PHE cc_start: 0.8600 (m-80) cc_final: 0.7877 (m-10)
REVERT: B   22 GLN cc_start: 0.8892 (mt0) cc_final: 0.8574 (pt0)
REVERT: B   79 GLU cc_start: 0.8475 (mp0) cc_final: 0.7914 (pm20)
REVERT: B  109 GLN cc_start: 0.8400 (tm-30) cc_final: 0.8054 (tm-30)
REVERT: B  110 GLN cc_start: 0.8949 (mt0) cc_final: 0.8471 (mp10)
REVERT: B  121 ASP cc_start: 0.9138 (t70) cc_final: 0.8488 (t0)
REVERT: B  133 TYR cc_start: 0.8221 (p90) cc_final: 0.8006 (p90)
REVERT: C   57 ASN cc_start: 0.8935 (m110) cc_final: 0.8652 (m110)
REVERT: C  112 MET cc_start: 0.8103 (tpp) cc_final: 0.7865 (tpp)
REVERT: C  190 HIS cc_start: 0.7835 (m-70) cc_final: 0.7382 (m170)
REVERT: C  192 PHE cc_start: 0.9009 (m-80) cc_final: 0.8720 (m-80)
REVERT: D   26 ASN cc_start: 0.9486 (t0) cc_final: 0.9166 (t0)
REVERT: D   28 ASP cc_start: 0.8388 (m-30) cc_final: 0.7994 (m-30)
REVERT: D  142 VAL cc_start: 0.8895 (m) cc_final: 0.8483 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 121
  average time/residue: 0.2251
  time to fit residues: 38.1390
Evaluate side-chains
  79 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 1.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 13 optimal weight:    0.0170
   chunk 22 optimal weight:   10.0000
   chunk 75 optimal weight:    3.9990
   chunk 73 optimal weight:    7.9990
   chunk 66 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 41 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9980
   chunk 63 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    1.1222

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

Flipped N/Q/H residues before XYZ refinement:
B 171 HIS
** C  26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  92 HIS
D 108 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.062210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.049796 restraints weight = 36368.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.051255 restraints weight = 21315.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.052222 restraints weight = 14512.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2913
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2913 r_free = 0.2913    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2913 r_free = 0.2913    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2913
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.3142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8547  Z= 0.225
  Angle     :  0.583   6.824  11955  Z= 0.343
  Chirality :  0.039   0.168   1371
  Planarity :  0.004   0.049   1203
  Dihedral  : 24.588  85.060   1969
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  :  4.24 %
    Favored  : 95.32 %
  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:  1.19 (0.30), residues: 796
  helix:  2.19 (0.24), residues: 434
  sheet: -0.75 (0.58), residues: 68
  loop : -1.00 (0.37), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 159 
 HIS   0.011   0.001   HIS A 171 
 PHE   0.019   0.002   PHE A 122 
 TYR   0.025   0.002   TYR C 206 
 ARG   0.004   0.001   ARG A  38 

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 102
  time to evaluate  : 1.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  207 PHE cc_start: 0.8566 (m-80) cc_final: 0.7711 (m-10)
REVERT: B   79 GLU cc_start: 0.8392 (mp0) cc_final: 0.7890 (pm20)
REVERT: B  133 TYR cc_start: 0.8394 (p90) cc_final: 0.7982 (p90)
REVERT: B  189 ASP cc_start: 0.7443 (m-30) cc_final: 0.7195 (m-30)
REVERT: C   57 ASN cc_start: 0.8842 (m110) cc_final: 0.8508 (m110)
REVERT: C  190 HIS cc_start: 0.7772 (m-70) cc_final: 0.7464 (m170)
REVERT: C  193 PHE cc_start: 0.8528 (p90) cc_final: 0.7996 (p90)
REVERT: D   26 ASN cc_start: 0.9400 (t0) cc_final: 0.9080 (t0)
REVERT: D   28 ASP cc_start: 0.8369 (m-30) cc_final: 0.7837 (m-30)
  outliers start: 3
  outliers final: 0
  residues processed: 104
  average time/residue: 0.2407
  time to fit residues: 35.5891
Evaluate side-chains
  71 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 57 optimal weight:    9.9990
   chunk 42 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 59 optimal weight:    8.9990
   chunk 69 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 73 optimal weight:    0.0670
   chunk 2 optimal weight:    4.9990
   overall best weight:    0.8120

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 171 HIS
C  26 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.061602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.048957 restraints weight = 36069.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.050538 restraints weight = 20356.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.051583 restraints weight = 13559.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2901
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2901 r_free = 0.2901    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2901 r_free = 0.2901    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2901
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.3539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8547  Z= 0.190
  Angle     :  0.551   7.234  11955  Z= 0.324
  Chirality :  0.038   0.191   1371
  Planarity :  0.003   0.037   1203
  Dihedral  : 24.199  74.269   1969
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  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:  1.27 (0.30), residues: 796
  helix:  2.17 (0.24), residues: 441
  sheet: -0.47 (0.63), residues: 67
  loop : -0.96 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP B 159 
 HIS   0.011   0.001   HIS B 171 
 PHE   0.019   0.002   PHE A 122 
 TYR   0.014   0.001   TYR B  88 
 ARG   0.003   0.000   ARG A  38 

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.815 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  112 MET cc_start: 0.9119 (tpp) cc_final: 0.8532 (mmm)
REVERT: A  162 THR cc_start: 0.8776 (p) cc_final: 0.7916 (p)
REVERT: B   79 GLU cc_start: 0.8479 (mp0) cc_final: 0.7915 (pm20)
REVERT: B  105 ILE cc_start: 0.9149 (mt) cc_final: 0.8780 (mt)
REVERT: B  133 TYR cc_start: 0.8137 (p90) cc_final: 0.7841 (p90)
REVERT: C   57 ASN cc_start: 0.8840 (m110) cc_final: 0.8488 (m110)
REVERT: D   26 ASN cc_start: 0.9371 (t0) cc_final: 0.9024 (t0)
REVERT: D   28 ASP cc_start: 0.8339 (m-30) cc_final: 0.7735 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.2020
  time to fit residues: 28.4792
Evaluate side-chains
  71 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 74 optimal weight:    5.9990
   chunk 57 optimal weight:    5.9990
   chunk 64 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 81 optimal weight:    4.9990
   chunk 66 optimal weight:    1.9990
   chunk 58 optimal weight:    9.9990
   chunk 28 optimal weight:    4.9990
   chunk 31 optimal weight:    0.6980
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 148 HIS
B 171 HIS
** C  26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 161 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.058931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2774 r_free = 0.2774 target = 0.046559 restraints weight = 36122.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2818 r_free = 0.2818 target = 0.048090 restraints weight = 20282.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.049105 restraints weight = 13535.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.2834
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2834
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2834 r_free = 0.2834    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2834 r_free = 0.2834    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2834
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.4106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8547  Z= 0.247
  Angle     :  0.574   5.575  11955  Z= 0.336
  Chirality :  0.040   0.196   1371
  Planarity :  0.004   0.046   1203
  Dihedral  : 23.713  65.415   1969
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  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:  1.35 (0.30), residues: 796
  helix:  2.18 (0.24), residues: 440
  sheet: -0.03 (0.66), residues: 68
  loop : -0.93 (0.38), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.003   TRP A 159 
 HIS   0.009   0.001   HIS A 171 
 PHE   0.021   0.002   PHE A 122 
 TYR   0.016   0.002   TYR A  13 
 ARG   0.006   0.001   ARG B 202 

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.743 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   79 GLU cc_start: 0.8507 (mp0) cc_final: 0.8138 (pm20)
REVERT: B  133 TYR cc_start: 0.8222 (p90) cc_final: 0.7937 (p90)
REVERT: B  189 ASP cc_start: 0.6904 (m-30) cc_final: 0.6584 (m-30)
REVERT: C   57 ASN cc_start: 0.8880 (m110) cc_final: 0.8549 (m110)
REVERT: D   26 ASN cc_start: 0.9307 (t0) cc_final: 0.8931 (t0)
REVERT: D   28 ASP cc_start: 0.8429 (m-30) cc_final: 0.7763 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 91
  average time/residue: 0.2124
  time to fit residues: 26.2087
Evaluate side-chains
  71 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.738 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 70 optimal weight:    0.5980
   chunk 6 optimal weight:    4.9990
   chunk 75 optimal weight:    2.9990
   chunk 86 optimal weight:    5.9990
   chunk 82 optimal weight:    3.9990
   chunk 79 optimal weight:    5.9990
   chunk 1 optimal weight:    0.7980
   chunk 32 optimal weight:    5.9990
   chunk 58 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   chunk 81 optimal weight:    4.9990
   overall best weight:    2.0786

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.056729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2706 r_free = 0.2706 target = 0.044214 restraints weight = 37294.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.045714 restraints weight = 21257.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.046712 restraints weight = 14304.225|
|-----------------------------------------------------------------------------|
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2769
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2769 r_free = 0.2769    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2769 r_free = 0.2769    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2769
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.4677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   8547  Z= 0.298
  Angle     :  0.608   8.056  11955  Z= 0.354
  Chirality :  0.042   0.201   1371
  Planarity :  0.004   0.038   1203
  Dihedral  : 23.215  63.553   1969
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  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:  1.17 (0.30), residues: 796
  helix:  2.08 (0.24), residues: 434
  sheet: -0.04 (0.67), residues: 68
  loop : -1.05 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 159 
 HIS   0.008   0.001   HIS A 171 
 PHE   0.018   0.002   PHE A 122 
 TYR   0.018   0.002   TYR A  13 
 ARG   0.008   0.001   ARG C 202 

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.839 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   79 GLU cc_start: 0.8588 (mp0) cc_final: 0.8170 (pm20)
REVERT: B  124 LEU cc_start: 0.8832 (mm) cc_final: 0.8363 (tp)
REVERT: C   57 ASN cc_start: 0.8829 (m110) cc_final: 0.8495 (m110)
REVERT: D   26 ASN cc_start: 0.9306 (t0) cc_final: 0.8860 (t0)
REVERT: D   28 ASP cc_start: 0.8520 (m-30) cc_final: 0.7712 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.1882
  time to fit residues: 23.1651
Evaluate side-chains
  64 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 66 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   chunk 55 optimal weight:    6.9990
   chunk 27 optimal weight:    0.2980
   chunk 63 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   chunk 79 optimal weight:    5.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
A 108 GLN
C  26 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.058211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2755 r_free = 0.2755 target = 0.045844 restraints weight = 36550.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.047308 restraints weight = 21264.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.048354 restraints weight = 14448.476|
|-----------------------------------------------------------------------------|
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2815
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2815 r_free = 0.2815    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2815 r_free = 0.2815    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2815
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.4690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8547  Z= 0.180
  Angle     :  0.537   7.115  11955  Z= 0.315
  Chirality :  0.039   0.148   1371
  Planarity :  0.003   0.038   1203
  Dihedral  : 23.152  60.379   1969
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.37 (0.31), residues: 796
  helix:  2.28 (0.24), residues: 434
  sheet: -0.05 (0.67), residues: 68
  loop : -0.99 (0.37), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 159 
 HIS   0.007   0.001   HIS A 171 
 PHE   0.015   0.001   PHE A 122 
 TYR   0.019   0.001   TYR C 206 
 ARG   0.005   0.000   ARG C 202 

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.864 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  112 MET cc_start: 0.9132 (tpp) cc_final: 0.8864 (tpp)
REVERT: B   79 GLU cc_start: 0.8595 (mp0) cc_final: 0.8148 (pm20)
REVERT: C   57 ASN cc_start: 0.8852 (m110) cc_final: 0.8523 (m110)
REVERT: C   86 ASN cc_start: 0.8325 (m110) cc_final: 0.8094 (m110)
REVERT: D   26 ASN cc_start: 0.9280 (t0) cc_final: 0.8809 (t0)
REVERT: D   28 ASP cc_start: 0.8511 (m-30) cc_final: 0.7653 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 86
  average time/residue: 0.2155
  time to fit residues: 25.3889
Evaluate side-chains
  67 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0000
   chunk 78 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 81 optimal weight:    4.9990
   chunk 18 optimal weight:    9.9990
   chunk 75 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 6 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    1.1788

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
C  26 ASN
** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 187 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 = 0.3084 r_free = 0.3084 target = 0.057776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.045270 restraints weight = 37164.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.046808 restraints weight = 21080.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.047876 restraints weight = 14108.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2806
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2806 r_free = 0.2806    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2806 r_free = 0.2806    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2806
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.4892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8547  Z= 0.213
  Angle     :  0.554   7.250  11955  Z= 0.324
  Chirality :  0.039   0.149   1371
  Planarity :  0.003   0.038   1203
  Dihedral  : 22.952  59.191   1969
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    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 (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:  1.33 (0.30), residues: 796
  helix:  2.24 (0.24), residues: 434
  sheet: -0.05 (0.67), residues: 68
  loop : -1.01 (0.37), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 159 
 HIS   0.007   0.001   HIS A 171 
 PHE   0.017   0.002   PHE D 122 
 TYR   0.013   0.001   TYR A  13 
 ARG   0.005   0.001   ARG C 202 

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.853 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   79 GLU cc_start: 0.8589 (mp0) cc_final: 0.8154 (pm20)
REVERT: B  124 LEU cc_start: 0.8785 (mm) cc_final: 0.8344 (tp)
REVERT: C   57 ASN cc_start: 0.8820 (m110) cc_final: 0.8486 (m110)
REVERT: C   86 ASN cc_start: 0.8265 (m110) cc_final: 0.7820 (m110)
REVERT: D   26 ASN cc_start: 0.9282 (t0) cc_final: 0.8805 (t0)
REVERT: D   28 ASP cc_start: 0.8526 (m-30) cc_final: 0.7648 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 89
  average time/residue: 0.2156
  time to fit residues: 26.9932
Evaluate side-chains
  66 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 83 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9980
   chunk 55 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   chunk 33 optimal weight:    0.5980
   chunk 20 optimal weight:    5.9990
   chunk 15 optimal weight:    4.9990
   chunk 60 optimal weight:    0.5980
   chunk 63 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
A 160 HIS
C  26 ASN
C 190 HIS
C 208 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.058600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.046160 restraints weight = 37093.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.047650 restraints weight = 21535.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.048674 restraints weight = 14590.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2828
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2828 r_free = 0.2828    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2828 r_free = 0.2828    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2828
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.4982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8547  Z= 0.185
  Angle     :  0.564   8.726  11955  Z= 0.326
  Chirality :  0.039   0.173   1371
  Planarity :  0.003   0.038   1203
  Dihedral  : 22.877  59.982   1969
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.73 %
    Favored  : 99.12 %
  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:  1.32 (0.30), residues: 796
  helix:  2.21 (0.24), residues: 434
  sheet: -0.05 (0.67), residues: 68
  loop : -0.97 (0.37), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.004   TRP A 159 
 HIS   0.006   0.001   HIS A 171 
 PHE   0.012   0.001   PHE A 122 
 TYR   0.019   0.001   TYR C 206 
 ARG   0.004   0.001   ARG C 202 

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 86
  time to evaluate  : 0.816 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   79 GLU cc_start: 0.8506 (mp0) cc_final: 0.8146 (pm20)
REVERT: B  124 LEU cc_start: 0.8809 (mm) cc_final: 0.8363 (tp)
REVERT: B  133 TYR cc_start: 0.8247 (p90) cc_final: 0.8000 (p90)
REVERT: C   57 ASN cc_start: 0.8792 (m110) cc_final: 0.8457 (m110)
REVERT: C   86 ASN cc_start: 0.8111 (m110) cc_final: 0.7705 (m110)
REVERT: C  190 HIS cc_start: 0.7863 (m-70) cc_final: 0.7599 (m170)
REVERT: C  208 ASN cc_start: 0.6575 (OUTLIER) cc_final: 0.6354 (p0)
REVERT: D   26 ASN cc_start: 0.9282 (t0) cc_final: 0.8798 (t0)
REVERT: D   28 ASP cc_start: 0.8542 (m-30) cc_final: 0.7641 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 87
  average time/residue: 0.1954
  time to fit residues: 23.8398
Evaluate side-chains
  68 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 67
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 38 optimal weight:    6.9990
   chunk 50 optimal weight:    0.9990
   chunk 85 optimal weight:    3.9990
   chunk 80 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 68 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 45 optimal weight:    5.9990
   chunk 59 optimal weight:   10.0000
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
** C  26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.056903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.044415 restraints weight = 37024.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2757 r_free = 0.2757 target = 0.045927 restraints weight = 21078.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2788 r_free = 0.2788 target = 0.046972 restraints weight = 14168.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.2777
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2777
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2777 r_free = 0.2777    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2777 r_free = 0.2777    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2777
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.5280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8547  Z= 0.264
  Angle     :  0.600   8.026  11955  Z= 0.346
  Chirality :  0.041   0.189   1371
  Planarity :  0.003   0.037   1203
  Dihedral  : 22.730  59.983   1969
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  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:  1.22 (0.30), residues: 796
  helix:  2.10 (0.24), residues: 434
  sheet: -0.28 (0.67), residues: 70
  loop : -0.92 (0.37), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.003   TRP A 159 
 HIS   0.007   0.001   HIS A 190 
 PHE   0.018   0.002   PHE D 207 
 TYR   0.024   0.002   TYR D  88 
 ARG   0.005   0.001   ARG D  53 

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.734 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   79 GLU cc_start: 0.8600 (mp0) cc_final: 0.8165 (pm20)
REVERT: B  124 LEU cc_start: 0.8827 (mm) cc_final: 0.8364 (tp)
REVERT: C   86 ASN cc_start: 0.8152 (m110) cc_final: 0.7661 (m110)
REVERT: C  190 HIS cc_start: 0.7922 (m-70) cc_final: 0.7721 (m170)
REVERT: D   26 ASN cc_start: 0.9235 (t0) cc_final: 0.8837 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.1948
  time to fit residues: 22.8456
Evaluate side-chains
  59 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9990
   chunk 42 optimal weight:    0.3980
   chunk 75 optimal weight:    0.8980
   chunk 18 optimal weight:    9.9990
   chunk 37 optimal weight:    0.0040
   chunk 34 optimal weight:    0.0050
   chunk 31 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 79 optimal weight:    6.9990
   overall best weight:    0.4206

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

Flipped N/Q/H residues before XYZ refinement:
A 108 GLN
** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  26 ASN
D  92 HIS
D 108 GLN
** D 187 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 = 0.3118 r_free = 0.3118 target = 0.058983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.046457 restraints weight = 36985.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2818 r_free = 0.2818 target = 0.047996 restraints weight = 21015.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.049060 restraints weight = 14120.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.2836
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2837
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2837 r_free = 0.2837    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2837 r_free = 0.2837    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2837
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.5251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8547  Z= 0.173
  Angle     :  0.569   8.573  11955  Z= 0.329
  Chirality :  0.040   0.217   1371
  Planarity :  0.003   0.038   1203
  Dihedral  : 22.709  59.811   1969
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  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:  1.30 (0.31), residues: 796
  helix:  2.20 (0.24), residues: 440
  sheet: -0.41 (0.66), residues: 70
  loop : -0.97 (0.37), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.004   TRP A 159 
 HIS   0.005   0.001   HIS A 171 
 PHE   0.022   0.001   PHE A 207 
 TYR   0.016   0.001   TYR D  88 
 ARG   0.004   0.001   ARG C 202 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2342.98 seconds
wall clock time: 43 minutes 11.28 seconds (2591.28 seconds total)