Starting phenix.real_space_refine
on Wed Mar  4 19:04:20 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xcz_33130/03_2026/7xcz_33130.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xcz_33130/03_2026/7xcz_33130.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xcz_33130/03_2026/7xcz_33130.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xcz_33130/03_2026/7xcz_33130.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xcz_33130/03_2026/7xcz_33130.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xcz_33130/03_2026/7xcz_33130.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.080
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
     S      30      5.16       5
     C    5093      2.51       5
     N    1369      2.21       5
     O    1597      1.98       5
     H    7747      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15836
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3023
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 196, 3023
          Classifications: {'peptide': 196}
          Modifications used: {'COO': 1, 'NH1NOTPRO': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 184}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 3281
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 3281
          Classifications: {'peptide': 224}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 212}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "E"
      Number of atoms: 3150
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 3150
          Classifications: {'peptide': 214}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 10
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 3208
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 3208
          Classifications: {'peptide': 220}
          Modifications used: {'COO': 1, 'NH1NOTPRO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 207}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLU%NH1NOTPRO:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "C"
      Number of atoms: 3174
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 3174
          Classifications: {'peptide': 215}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 201}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 5
  Time building chain proxies: 3.00, per 1000 atoms: 0.19
  Number of scatterers: 15836
  At special positions: 0
  Unit cell: (81.472, 145.792, 124.352, 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      30     16.00
     O    1597      8.00
     N    1369      7.00
     C    5093      6.00
     H    7747      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 362 " - pdb=" SG  CYS A 415 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 374 " - pdb=" SG  CYS A 508 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 148 " - pdb=" SG  CYS D 204 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 224 " - pdb=" SG  CYS E 214 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 134 " - pdb=" SG  CYS E 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  95 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 141 " - pdb=" SG  CYS B 197 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C  89 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 135 " - pdb=" SG  CYS C 195 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.25
  Conformation dependent library (CDL) restraints added in 502.6 milliseconds
  

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1972

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 22 sheets defined
      6.5% alpha, 38.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 332 through 336
      removed outlier: 3.929A  pdb=" N   TRP A 336 " --> pdb=" O   VAL A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 348 through 353
      removed outlier: 3.638A  pdb=" N   TYR A 352 " --> pdb=" O   TYR A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 399 through 405
    Processing helix  chain 'D' and resid 87 through 91
      removed outlier: 3.787A  pdb=" N   THR D  91 " --> pdb=" O   ALA D  88 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 135 through 139
      removed outlier: 3.514A  pdb=" N   THR D 139 " --> pdb=" O   SER D 136 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 121 through 128
      removed outlier: 3.895A  pdb=" N   LEU E 125 " --> pdb=" O   SER E 121 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 183 through 187
    Processing helix  chain 'B' and resid 157 through 159
      No H-bonds generated for 'chain 'B' and resid 157 through 159'
    Processing helix  chain 'C' and resid 80 through 84
      removed outlier: 3.685A  pdb=" N   PHE C  84 " --> pdb=" O   PRO C  81 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 122 through 129
      removed outlier: 3.503A  pdb=" N   LEU C 126 " --> pdb=" O   SER C 122 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 183 through 190
      removed outlier: 3.822A  pdb=" N   HIS C 190 " --> pdb=" O   ASP C 186 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 337 through 341
    Processing sheet with id=AA2, first strand: chain 'A' and resid 435 through 437
    Processing sheet with id=AA3, first strand: chain 'A' and resid 456 through 457
    Processing sheet with id=AA4, first strand: chain 'D' and resid 3 through 7
    Processing sheet with id=AA5, first strand: chain 'D' and resid 58 through 60
      removed outlier: 6.536A  pdb=" N   TRP D  36 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   VAL D  50 " --> pdb=" O   MET D  34 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   MET D  34 " --> pdb=" O   VAL D  50 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   VAL D 110 " --> pdb=" O   ARG D  98 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 58 through 60
      removed outlier: 6.536A  pdb=" N   TRP D  36 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   VAL D  50 " --> pdb=" O   MET D  34 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   MET D  34 " --> pdb=" O   VAL D  50 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 128 through 132
      removed outlier: 6.010A  pdb=" N   TYR D 184 " --> pdb=" O   ASP D 152 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 159 through 162
    Processing sheet with id=AA9, first strand: chain 'E' and resid 5 through 7
      removed outlier: 3.767A  pdb=" N   ALA E  25 " --> pdb=" O   THR E  69 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   THR E  69 " --> pdb=" O   ALA E  25 " (cutoff:3.500A)
      removed outlier: 10.362A  pdb=" N   GLN E  27 " --> pdb=" O   SER E  67 " (cutoff:3.500A)
      removed outlier: 9.884A  pdb=" N   SER E  67 " --> pdb=" O   GLN E  27 " (cutoff:3.500A)
      removed outlier: 11.973A  pdb=" N   ILE E  29 " --> pdb=" O   SER E  65 " (cutoff:3.500A)
      removed outlier: 11.636A  pdb=" N   SER E  65 " --> pdb=" O   ILE E  29 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 13
      removed outlier: 6.856A  pdb=" N   VAL E  11 " --> pdb=" O   ASP E 105 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   TRP E  35 " --> pdb=" O   LEU E  47 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 13
      removed outlier: 6.856A  pdb=" N   VAL E  11 " --> pdb=" O   ASP E 105 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   SER E  97 " --> pdb=" O   GLN E  90 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 116 through 118
      removed outlier: 5.989A  pdb=" N   TYR E 173 " --> pdb=" O   ASN E 138 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 153 through 154
      removed outlier: 3.812A  pdb=" N   VAL E 205 " --> pdb=" O   VAL E 196 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 3 through 8
    Processing sheet with id=AB6, first strand: chain 'B' and resid 57 through 59
      removed outlier: 3.615A  pdb=" N   SER B  40 " --> pdb=" O   GLY B  44 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   TRP B  36 " --> pdb=" O   ILE B  48 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   GLN B  50 " --> pdb=" O   TRP B  34 " (cutoff:3.500A)
      removed outlier: 6.046A  pdb=" N   TRP B  34 " --> pdb=" O   GLN B  50 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 121 through 125
      removed outlier: 6.001A  pdb=" N   TYR B 177 " --> pdb=" O   ASP B 145 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 152 through 155
      removed outlier: 4.464A  pdb=" N   TYR B 195 " --> pdb=" O   VAL B 212 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LYS B 210 " --> pdb=" O   CYS B 197 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 4 through 7
    Processing sheet with id=AC1, first strand: chain 'C' and resid 10 through 13
    Processing sheet with id=AC2, first strand: chain 'C' and resid 54 through 55
      removed outlier: 6.661A  pdb=" N   TRP C  36 " --> pdb=" O   LEU C  48 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   THR C  98 " --> pdb=" O   GLN C  91 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'C' and resid 115 through 119
      removed outlier: 3.668A  pdb=" N   VAL C 134 " --> pdb=" O   PHE C 119 " (cutoff:3.500A)
      removed outlier: 5.907A  pdb=" N   TYR C 174 " --> pdb=" O   ASN C 139 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'C' and resid 145 through 150

    304 hydrogen bonds defined for protein.
    759 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.69

  Time building geometry restraints manager: 1.78 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 7747
        1.03 -     1.23: 103
        1.23 -     1.43: 3471
        1.43 -     1.62: 4675
        1.62 -     1.82: 36
  Bond restraints: 16032
  Sorted by residual:
  bond pdb=" N   THR A 316 "
       pdb=" H1  THR A 316 "
    ideal  model  delta    sigma   weight residual
    0.960  0.861  0.099 2.00e-02 2.50e+03 2.47e+01
  bond pdb=" N   GLU B   1 "
       pdb=" H1  GLU B   1 "
    ideal  model  delta    sigma   weight residual
    0.960  0.861  0.099 2.00e-02 2.50e+03 2.47e+01
  bond pdb=" N   ASP E   1 "
       pdb=" H2  ASP E   1 "
    ideal  model  delta    sigma   weight residual
    0.890  0.960 -0.070 2.00e-02 2.50e+03 1.24e+01
  bond pdb=" N   GLU C   1 "
       pdb=" H3  GLU C   1 "
    ideal  model  delta    sigma   weight residual
    0.890  0.960 -0.070 2.00e-02 2.50e+03 1.24e+01
  bond pdb=" N   GLU D   1 "
       pdb=" H3  GLU D   1 "
    ideal  model  delta    sigma   weight residual
    0.890  0.960 -0.070 2.00e-02 2.50e+03 1.23e+01
  ... (remaining 16027 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    20.95: 28834
       20.95 -    41.90: 10
       41.90 -    62.85: 0
       62.85 -    83.80: 1
       83.80 -   104.75: 2
  Bond angle restraints: 28847
  Sorted by residual:
  angle pdb=" H1  GLU C   1 "
        pdb=" N   GLU C   1 "
        pdb=" H3  GLU C   1 "
      ideal   model   delta    sigma   weight residual
     109.47    4.72  104.75 3.00e+00 1.11e-01 1.22e+03
  angle pdb=" H1  ASP E   1 "
        pdb=" N   ASP E   1 "
        pdb=" H2  ASP E   1 "
      ideal   model   delta    sigma   weight residual
     109.47    9.03  100.44 3.00e+00 1.11e-01 1.12e+03
  angle pdb=" H1  GLU D   1 "
        pdb=" N   GLU D   1 "
        pdb=" H2  GLU D   1 "
      ideal   model   delta    sigma   weight residual
     109.47   25.92   83.55 3.00e+00 1.11e-01 7.76e+02
  angle pdb=" N   VAL A 428 "
        pdb=" CA  VAL A 428 "
        pdb=" HA  VAL A 428 "
      ideal   model   delta    sigma   weight residual
     110.00   73.93   36.07 3.00e+00 1.11e-01 1.45e+02
  angle pdb=" C   VAL A 428 "
        pdb=" CA  VAL A 428 "
        pdb=" HA  VAL A 428 "
      ideal   model   delta    sigma   weight residual
     109.00   73.24   35.76 3.00e+00 1.11e-01 1.42e+02
  ... (remaining 28842 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.33: 6804
       17.33 -    34.65: 666
       34.65 -    51.98: 210
       51.98 -    69.30: 64
       69.30 -    86.63: 12
  Dihedral angle restraints: 7756
    sinusoidal: 4102
      harmonic: 3654
  Sorted by residual:
  dihedral pdb=" CB  CYS B  22 "
           pdb=" SG  CYS B  22 "
           pdb=" SG  CYS B  95 "
           pdb=" CB  CYS B  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   49.04   43.96     1      1.00e+01 1.00e-02 2.69e+01
  dihedral pdb=" CB  CYS E 134 "
           pdb=" SG  CYS E 134 "
           pdb=" SG  CYS E 194 "
           pdb=" CB  CYS E 194 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   50.02   42.98     1      1.00e+01 1.00e-02 2.58e+01
  dihedral pdb=" CA  SER C  30 "
           pdb=" C   SER C  30 "
           pdb=" N   SER C  31 "
           pdb=" CA  SER C  31 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.26  -22.74     0      5.00e+00 4.00e-02 2.07e+01
  ... (remaining 7753 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 1137
       0.078 -    0.157: 106
       0.157 -    0.235: 1
       0.235 -    0.314: 0
       0.314 -    0.392: 2
  Chirality restraints: 1246
  Sorted by residual:
  chirality pdb=" CA  THR D 103 "
            pdb=" N   THR D 103 "
            pdb=" C   THR D 103 "
            pdb=" CB  THR D 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.13    0.39 2.00e-01 2.50e+01 3.85e+00
  chirality pdb=" CA  THR D 102 "
            pdb=" N   THR D 102 "
            pdb=" C   THR D 102 "
            pdb=" CB  THR D 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.20    0.33 2.00e-01 2.50e+01 2.69e+00
  chirality pdb=" CA  VAL A 428 "
            pdb=" N   VAL A 428 "
            pdb=" C   VAL A 428 "
            pdb=" CB  VAL A 428 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.22    0.23 2.00e-01 2.50e+01 1.27e+00
  ... (remaining 1243 not shown)

  Planarity restraints: 2465
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL D 192 "   -0.022 5.00e-02 4.00e+02   3.38e-02 1.82e+00
        pdb=" N   PRO D 193 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO D 193 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO D 193 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 167 "   -0.022 5.00e-02 4.00e+02   3.37e-02 1.81e+00
        pdb=" N   PRO B 168 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO B 168 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 168 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU D 156 "   -0.020 5.00e-02 4.00e+02   3.09e-02 1.52e+00
        pdb=" N   PRO D 157 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO D 157 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO D 157 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 2462 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.19: 1038
        2.19 -     2.79: 31778
        2.79 -     3.40: 38663
        3.40 -     4.00: 55240
        4.00 -     4.60: 84984
  Nonbonded interactions: 211703
  Sorted by model distance:
  nonbonded pdb=" O   SER D  52 "
            pdb="HH12 ARG D  72 "
     model   vdw
     1.591 2.450
  nonbonded pdb="HH11 ARG A 329 "
            pdb=" O   ALA E  91 "
     model   vdw
     1.596 2.450
  nonbonded pdb=" HE  ARG B  97 "
            pdb=" OD2 ASP B 102 "
     model   vdw
     1.622 2.450
  nonbonded pdb=" H   ASP E 151 "
            pdb=" O   VAL E 191 "
     model   vdw
     1.623 2.450
  nonbonded pdb="HH21 ARG D  98 "
            pdb=" OD2 ASP D 109 "
     model   vdw
     1.637 2.450
  ... (remaining 211698 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             3.560
  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:             0.090
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     16.350
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
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      :  0.004   0.042   8295  Z= 0.183
  Angle     :  0.510   4.588  11292  Z= 0.275
  Chirality :  0.045   0.392   1246
  Planarity :  0.003   0.034   1460
  Dihedral  : 15.749  86.629   2942
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.12 %
    Favored  : 91.78 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 24.10 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.95 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.76 (0.22), residues: 1059
  helix: -4.98 (0.16), residues: 54
  sheet: -1.35 (0.22), residues: 450
  loop : -3.32 (0.22), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  72 
 TYR   0.010   0.001   TYR D  95 
 PHE   0.011   0.001   PHE B  78 
 TRP   0.007   0.001   TRP B 155 
 HIS   0.002   0.001   HIS D  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 ( 8285)
  covalent geometry    : angle       0.50989 (11272)
  SS BOND              : bond        0.00266 (   10)
  SS BOND              : angle       0.63184 (   20)
  hydrogen bonds       : bond        0.11378 (  289)
  hydrogen bonds       : angle       7.32415 (  759)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  316 is missing expected H atoms. Skipping.
Residue SER  382 is missing expected H atoms. Skipping.
Residue SER  187 is missing expected H atoms. Skipping.
Residue THR    5 is missing expected H atoms. Skipping.
Residue SER  131 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  136 is missing expected H atoms. Skipping.
Residue VAL  146 is missing expected H atoms. Skipping.
Residue VAL  191 is missing expected H atoms. Skipping.
Residue LEU   18 is missing expected H atoms. Skipping.
Residue THR   21 is missing expected H atoms. Skipping.
Residue LEU   45 is missing expected H atoms. Skipping.
Residue THR  108 is missing expected H atoms. Skipping.
Residue THR  152 is missing expected H atoms. Skipping.
Residue SER  154 is missing expected H atoms. Skipping.
Residue SER  180 is missing expected H atoms. Skipping.
Residue LEU   21 is missing expected H atoms. Skipping.
Residue THR   98 is missing expected H atoms. Skipping.
Residue ILE  118 is missing expected H atoms. Skipping.
Residue SER  160 is missing expected H atoms. Skipping.
Residue THR  165 is missing expected H atoms. Skipping.
Residue VAL  192 is missing expected H atoms. Skipping.
Evaluate side-chains
  157 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 149
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  404 TYR cc_start: 0.8693 (m-10) cc_final: 0.8355 (m-10)
REVERT: D  150 VAL cc_start: 0.8224 (t) cc_final: 0.8023 (t)
REVERT: E   81 GLU cc_start: 0.7442 (pm20) cc_final: 0.7232 (pm20)
REVERT: E  170 ASP cc_start: 0.7454 (p0) cc_final: 0.7118 (p0)
REVERT: B   11 LEU cc_start: 0.8741 (tp) cc_final: 0.8337 (mt)
  outliers start: 8
  outliers final: 4
  residues processed: 156
  average time/residue: 0.2167
  time to fit residues: 45.4809
Evaluate side-chains
  114 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 110
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain B residue  217 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    3.9990
   chunk 38 optimal weight:    0.0010
   chunk 61 optimal weight:    7.9990
   overall best weight:    0.7188

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

Flipped N/Q/H residues before XYZ refinement:
A 476 GLN
A 481 GLN
E 124 GLN
E 198 HIS
B  50 GLN
B  58 ASN
B 156 ASN
C   6 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.137938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.103275 restraints weight = 30208.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3110 rms_B_bonded: 2.10
r_work: 0.2966 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2840 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.1442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8295  Z= 0.134
  Angle     :  0.514   4.789  11292  Z= 0.270
  Chirality :  0.047   0.404   1246
  Planarity :  0.004   0.040   1460
  Dihedral  :  4.586  39.399   1157
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.70 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 23.31 %
    Favored  : 75.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.95 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.92 (0.24), residues: 1059
  helix: -4.58 (0.23), residues: 55
  sheet: -0.83 (0.23), residues: 456
  loop : -2.70 (0.24), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  72 
 TYR   0.011   0.001   TYR D  95 
 PHE   0.010   0.001   PHE B  78 
 TRP   0.008   0.001   TRP B  47 
 HIS   0.003   0.001   HIS B 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 8285)
  covalent geometry    : angle       0.51170 (11272)
  SS BOND              : bond        0.00234 (   10)
  SS BOND              : angle       1.33425 (   20)
  hydrogen bonds       : bond        0.03207 (  289)
  hydrogen bonds       : angle       5.98054 (  759)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  316 is missing expected H atoms. Skipping.
Residue SER  382 is missing expected H atoms. Skipping.
Residue SER  187 is missing expected H atoms. Skipping.
Residue THR    5 is missing expected H atoms. Skipping.
Residue SER  131 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  136 is missing expected H atoms. Skipping.
Residue VAL  146 is missing expected H atoms. Skipping.
Residue VAL  191 is missing expected H atoms. Skipping.
Residue LEU   18 is missing expected H atoms. Skipping.
Residue THR   21 is missing expected H atoms. Skipping.
Residue LEU   45 is missing expected H atoms. Skipping.
Residue THR  108 is missing expected H atoms. Skipping.
Residue THR  152 is missing expected H atoms. Skipping.
Residue SER  154 is missing expected H atoms. Skipping.
Residue SER  180 is missing expected H atoms. Skipping.
Residue LEU   21 is missing expected H atoms. Skipping.
Residue THR   98 is missing expected H atoms. Skipping.
Residue ILE  118 is missing expected H atoms. Skipping.
Residue SER  160 is missing expected H atoms. Skipping.
Residue THR  165 is missing expected H atoms. Skipping.
Residue VAL  192 is missing expected H atoms. Skipping.
Evaluate side-chains
  120 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 110
  time to evaluate  : 0.440 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  412 PHE cc_start: 0.8010 (OUTLIER) cc_final: 0.6934 (p90)
REVERT: D  150 VAL cc_start: 0.8319 (t) cc_final: 0.8107 (t)
REVERT: E  170 ASP cc_start: 0.7904 (p0) cc_final: 0.7440 (p0)
REVERT: B   11 LEU cc_start: 0.8992 (tp) cc_final: 0.8543 (mt)
  outliers start: 10
  outliers final: 4
  residues processed: 119
  average time/residue: 0.2013
  time to fit residues: 33.1220
Evaluate side-chains
  109 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 104
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  412 PHE
Chi-restraints excluded: chain D residue   96 CYS
Chi-restraints excluded: chain D residue  104 THR
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain E residue   30 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 37 optimal weight:    0.7980
   chunk 56 optimal weight:    8.9990
   chunk 73 optimal weight:    0.5980
   chunk 41 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 17 optimal weight:    0.1980
   chunk 93 optimal weight:    0.0980
   chunk 100 optimal weight:    3.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 423 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.138355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.102557 restraints weight = 30295.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.3100 rms_B_bonded: 2.03
r_work: 0.2952 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2825 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.2024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8295  Z= 0.105
  Angle     :  0.488   4.726  11292  Z= 0.255
  Chirality :  0.046   0.405   1246
  Planarity :  0.004   0.034   1460
  Dihedral  :  4.293  36.463   1154
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 2.46
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.14 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 22.41 %
    Favored  : 75.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.95 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.20 (0.25), residues: 1059
  helix: -4.04 (0.36), residues: 55
  sheet: -0.40 (0.23), residues: 457
  loop : -2.16 (0.25), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  18 
 TYR   0.007   0.001   TYR D  95 
 PHE   0.013   0.001   PHE E 116 
 TRP   0.010   0.001   TRP D  47 
 HIS   0.003   0.001   HIS B 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 8285)
  covalent geometry    : angle       0.48613 (11272)
  SS BOND              : bond        0.00214 (   10)
  SS BOND              : angle       0.99452 (   20)
  hydrogen bonds       : bond        0.02798 (  289)
  hydrogen bonds       : angle       5.57826 (  759)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  316 is missing expected H atoms. Skipping.
Residue SER  382 is missing expected H atoms. Skipping.
Residue SER  187 is missing expected H atoms. Skipping.
Residue THR    5 is missing expected H atoms. Skipping.
Residue SER  131 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  136 is missing expected H atoms. Skipping.
Residue VAL  146 is missing expected H atoms. Skipping.
Residue VAL  191 is missing expected H atoms. Skipping.
Residue LEU   18 is missing expected H atoms. Skipping.
Residue THR   21 is missing expected H atoms. Skipping.
Residue LEU   45 is missing expected H atoms. Skipping.
Residue THR  108 is missing expected H atoms. Skipping.
Residue THR  152 is missing expected H atoms. Skipping.
Residue SER  154 is missing expected H atoms. Skipping.
Residue SER  180 is missing expected H atoms. Skipping.
Residue LEU   21 is missing expected H atoms. Skipping.
Residue THR   98 is missing expected H atoms. Skipping.
Residue ILE  118 is missing expected H atoms. Skipping.
Residue SER  160 is missing expected H atoms. Skipping.
Residue THR  165 is missing expected H atoms. Skipping.
Residue VAL  192 is missing expected H atoms. Skipping.
Evaluate side-chains
  121 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  412 PHE cc_start: 0.8165 (OUTLIER) cc_final: 0.7037 (p90)
REVERT: D  146 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7228 (pp)
REVERT: D  150 VAL cc_start: 0.8300 (t) cc_final: 0.8080 (t)
REVERT: D  179 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.7163 (mp10)
REVERT: E   81 GLU cc_start: 0.7978 (pm20) cc_final: 0.7650 (pm20)
REVERT: E  170 ASP cc_start: 0.8010 (p0) cc_final: 0.7578 (p0)
REVERT: B   11 LEU cc_start: 0.9070 (tp) cc_final: 0.8644 (mt)
REVERT: B   81 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8244 (mtmm)
REVERT: C   82 GLU cc_start: 0.8402 (mp0) cc_final: 0.8022 (pm20)
  outliers start: 15
  outliers final: 4
  residues processed: 120
  average time/residue: 0.2078
  time to fit residues: 34.0810
Evaluate side-chains
  108 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  412 PHE
Chi-restraints excluded: chain A residue  442 SER
Chi-restraints excluded: chain D residue   96 CYS
Chi-restraints excluded: chain D residue  146 LEU
Chi-restraints excluded: chain D residue  179 GLN
Chi-restraints excluded: chain D residue  205 ASN
Chi-restraints excluded: chain B residue   81 LYS
Chi-restraints excluded: chain C residue   64 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 90 optimal weight:    4.9990
   chunk 0 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 50 optimal weight:    0.4980
   chunk 61 optimal weight:    0.9980
   chunk 82 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 56 optimal weight:    8.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
E  79 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.136004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.101405 restraints weight = 30072.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.3077 rms_B_bonded: 2.12
r_work: 0.2903 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2776 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.2776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.2408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8295  Z= 0.149
  Angle     :  0.506   5.079  11292  Z= 0.266
  Chirality :  0.046   0.407   1246
  Planarity :  0.004   0.035   1460
  Dihedral  :  4.348  41.226   1153
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 2.59
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.27 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 22.97 %
    Favored  : 75.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.95 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.83 (0.25), residues: 1059
  helix: -3.91 (0.39), residues: 55
  sheet: -0.13 (0.24), residues: 460
  loop : -1.92 (0.26), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  24 
 TYR   0.009   0.001   TYR B  94 
 PHE   0.009   0.001   PHE E 116 
 TRP   0.009   0.001   TRP B 155 
 HIS   0.003   0.001   HIS E 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 8285)
  covalent geometry    : angle       0.50511 (11272)
  SS BOND              : bond        0.00304 (   10)
  SS BOND              : angle       1.00771 (   20)
  hydrogen bonds       : bond        0.02865 (  289)
  hydrogen bonds       : angle       5.54204 (  759)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  316 is missing expected H atoms. Skipping.
Residue SER  382 is missing expected H atoms. Skipping.
Residue SER  187 is missing expected H atoms. Skipping.
Residue THR    5 is missing expected H atoms. Skipping.
Residue SER  131 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  136 is missing expected H atoms. Skipping.
Residue VAL  146 is missing expected H atoms. Skipping.
Residue VAL  191 is missing expected H atoms. Skipping.
Residue LEU   18 is missing expected H atoms. Skipping.
Residue THR   21 is missing expected H atoms. Skipping.
Residue LEU   45 is missing expected H atoms. Skipping.
Residue THR  108 is missing expected H atoms. Skipping.
Residue THR  152 is missing expected H atoms. Skipping.
Residue SER  154 is missing expected H atoms. Skipping.
Residue SER  180 is missing expected H atoms. Skipping.
Residue LEU   21 is missing expected H atoms. Skipping.
Residue THR   98 is missing expected H atoms. Skipping.
Residue ILE  118 is missing expected H atoms. Skipping.
Residue SER  160 is missing expected H atoms. Skipping.
Residue THR  165 is missing expected H atoms. Skipping.
Residue VAL  192 is missing expected H atoms. Skipping.
Evaluate side-chains
  120 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  412 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.7301 (p90)
REVERT: D   16 ARG cc_start: 0.8198 (mmm-85) cc_final: 0.7976 (mtp85)
REVERT: D  150 VAL cc_start: 0.8331 (t) cc_final: 0.8116 (t)
REVERT: D  179 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.7117 (mp10)
REVERT: E  170 ASP cc_start: 0.8096 (p0) cc_final: 0.7657 (p0)
REVERT: B   11 LEU cc_start: 0.9009 (tp) cc_final: 0.8596 (mt)
REVERT: C   82 GLU cc_start: 0.8456 (mp0) cc_final: 0.8067 (pm20)
  outliers start: 15
  outliers final: 9
  residues processed: 118
  average time/residue: 0.1977
  time to fit residues: 32.3966
Evaluate side-chains
  110 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  412 PHE
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain A residue  442 SER
Chi-restraints excluded: chain D residue   96 CYS
Chi-restraints excluded: chain D residue  104 THR
Chi-restraints excluded: chain D residue  179 GLN
Chi-restraints excluded: chain D residue  205 ASN
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain B residue  121 SER
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain C residue   64 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 99 optimal weight:    4.9990
   chunk 88 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   chunk 100 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 54 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
B   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.135818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.100207 restraints weight = 30231.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.3054 rms_B_bonded: 2.16
r_work: 0.2890 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2762 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.2671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8295  Z= 0.144
  Angle     :  0.501   4.998  11292  Z= 0.263
  Chirality :  0.046   0.407   1246
  Planarity :  0.004   0.035   1460
  Dihedral  :  4.355  40.937   1153
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 2.59
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.33 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 21.40 %
    Favored  : 76.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.95 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.62 (0.25), residues: 1059
  helix: -3.69 (0.44), residues: 55
  sheet: -0.01 (0.24), residues: 460
  loop : -1.77 (0.26), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  72 
 TYR   0.008   0.001   TYR E  86 
 PHE   0.009   0.001   PHE B  78 
 TRP   0.010   0.001   TRP B 155 
 HIS   0.004   0.001   HIS C 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 8285)
  covalent geometry    : angle       0.49930 (11272)
  SS BOND              : bond        0.00224 (   10)
  SS BOND              : angle       0.96487 (   20)
  hydrogen bonds       : bond        0.02883 (  289)
  hydrogen bonds       : angle       5.50900 (  759)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  316 is missing expected H atoms. Skipping.
Residue SER  382 is missing expected H atoms. Skipping.
Residue SER  187 is missing expected H atoms. Skipping.
Residue THR    5 is missing expected H atoms. Skipping.
Residue SER  131 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  136 is missing expected H atoms. Skipping.
Residue VAL  146 is missing expected H atoms. Skipping.
Residue VAL  191 is missing expected H atoms. Skipping.
Residue LEU   18 is missing expected H atoms. Skipping.
Residue THR   21 is missing expected H atoms. Skipping.
Residue LEU   45 is missing expected H atoms. Skipping.
Residue THR  108 is missing expected H atoms. Skipping.
Residue THR  152 is missing expected H atoms. Skipping.
Residue SER  154 is missing expected H atoms. Skipping.
Residue SER  180 is missing expected H atoms. Skipping.
Residue LEU   21 is missing expected H atoms. Skipping.
Residue THR   98 is missing expected H atoms. Skipping.
Residue ILE  118 is missing expected H atoms. Skipping.
Residue SER  160 is missing expected H atoms. Skipping.
Residue THR  165 is missing expected H atoms. Skipping.
Residue VAL  192 is missing expected H atoms. Skipping.
Evaluate side-chains
  128 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 106
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  412 PHE cc_start: 0.8560 (OUTLIER) cc_final: 0.7505 (p90)
REVERT: D  146 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7368 (pp)
REVERT: D  150 VAL cc_start: 0.8307 (t) cc_final: 0.8095 (t)
REVERT: D  179 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.7117 (mp10)
REVERT: E   81 GLU cc_start: 0.8257 (pm20) cc_final: 0.7827 (pm20)
REVERT: E  170 ASP cc_start: 0.8145 (p0) cc_final: 0.7699 (p0)
REVERT: B   11 LEU cc_start: 0.9007 (tp) cc_final: 0.8598 (mt)
REVERT: B   81 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8301 (mtmm)
REVERT: C   82 GLU cc_start: 0.8492 (mp0) cc_final: 0.7939 (pm20)
  outliers start: 22
  outliers final: 15
  residues processed: 125
  average time/residue: 0.1915
  time to fit residues: 33.4588
Evaluate side-chains
  114 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  412 PHE
Chi-restraints excluded: chain A residue  413 THR
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain A residue  442 SER
Chi-restraints excluded: chain D residue   96 CYS
Chi-restraints excluded: chain D residue  104 THR
Chi-restraints excluded: chain D residue  146 LEU
Chi-restraints excluded: chain D residue  149 LEU
Chi-restraints excluded: chain D residue  179 GLN
Chi-restraints excluded: chain D residue  205 ASN
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   33 LEU
Chi-restraints excluded: chain B residue   81 LYS
Chi-restraints excluded: chain B residue  121 SER
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain C residue   27 GLN
Chi-restraints excluded: chain C residue   64 SER
Chi-restraints excluded: chain C residue   71 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 40 optimal weight:    0.5980
   chunk 70 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 94 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    0.7980
   chunk 96 optimal weight:    0.0010
   chunk 64 optimal weight:    0.9990
   chunk 93 optimal weight:    0.9980
   chunk 81 optimal weight:    0.7980
   overall best weight:    0.6186

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

Flipped N/Q/H residues before XYZ refinement:
B   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.136745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.102175 restraints weight = 30141.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3090 rms_B_bonded: 2.16
r_work: 0.2914 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2785 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.2866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8295  Z= 0.112
  Angle     :  0.481   4.876  11292  Z= 0.252
  Chirality :  0.046   0.405   1246
  Planarity :  0.004   0.034   1460
  Dihedral  :  4.224  38.085   1153
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 2.78
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.52 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 21.51 %
    Favored  : 76.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.95 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.40 (0.25), residues: 1059
  helix: -3.42 (0.50), residues: 55
  sheet:  0.12 (0.24), residues: 460
  loop : -1.62 (0.26), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  72 
 TYR   0.008   0.001   TYR A 352 
 PHE   0.011   0.001   PHE E 116 
 TRP   0.008   0.001   TRP B 155 
 HIS   0.004   0.001   HIS C 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 8285)
  covalent geometry    : angle       0.47945 (11272)
  SS BOND              : bond        0.00285 (   10)
  SS BOND              : angle       0.92800 (   20)
  hydrogen bonds       : bond        0.02700 (  289)
  hydrogen bonds       : angle       5.35495 (  759)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  316 is missing expected H atoms. Skipping.
Residue SER  382 is missing expected H atoms. Skipping.
Residue SER  187 is missing expected H atoms. Skipping.
Residue THR    5 is missing expected H atoms. Skipping.
Residue SER  131 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  136 is missing expected H atoms. Skipping.
Residue VAL  146 is missing expected H atoms. Skipping.
Residue VAL  191 is missing expected H atoms. Skipping.
Residue LEU   18 is missing expected H atoms. Skipping.
Residue THR   21 is missing expected H atoms. Skipping.
Residue LEU   45 is missing expected H atoms. Skipping.
Residue THR  108 is missing expected H atoms. Skipping.
Residue THR  152 is missing expected H atoms. Skipping.
Residue SER  154 is missing expected H atoms. Skipping.
Residue SER  180 is missing expected H atoms. Skipping.
Residue LEU   21 is missing expected H atoms. Skipping.
Residue THR   98 is missing expected H atoms. Skipping.
Residue ILE  118 is missing expected H atoms. Skipping.
Residue SER  160 is missing expected H atoms. Skipping.
Residue THR  165 is missing expected H atoms. Skipping.
Residue VAL  192 is missing expected H atoms. Skipping.
Evaluate side-chains
  119 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  412 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.7369 (p90)
REVERT: D  146 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7394 (pp)
REVERT: D  150 VAL cc_start: 0.8288 (t) cc_final: 0.8074 (t)
REVERT: D  179 GLN cc_start: 0.7459 (OUTLIER) cc_final: 0.7093 (mp10)
REVERT: E   81 GLU cc_start: 0.8156 (pm20) cc_final: 0.7912 (pm20)
REVERT: E  170 ASP cc_start: 0.7992 (p0) cc_final: 0.7540 (p0)
REVERT: B   11 LEU cc_start: 0.9038 (tp) cc_final: 0.8621 (mt)
REVERT: B   81 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8302 (mtmm)
REVERT: C   82 GLU cc_start: 0.8488 (mp0) cc_final: 0.7915 (pm20)
  outliers start: 17
  outliers final: 13
  residues processed: 118
  average time/residue: 0.1720
  time to fit residues: 29.0020
Evaluate side-chains
  116 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  412 PHE
Chi-restraints excluded: chain A residue  413 THR
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain A residue  442 SER
Chi-restraints excluded: chain D residue   96 CYS
Chi-restraints excluded: chain D residue  104 THR
Chi-restraints excluded: chain D residue  146 LEU
Chi-restraints excluded: chain D residue  149 LEU
Chi-restraints excluded: chain D residue  179 GLN
Chi-restraints excluded: chain D residue  205 ASN
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain B residue   81 LYS
Chi-restraints excluded: chain B residue  121 SER
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain C residue   64 SER
Chi-restraints excluded: chain C residue   71 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0370
   chunk 90 optimal weight:    3.9990
   chunk 101 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0470
   chunk 37 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 104 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 24 optimal weight:    0.1980
   overall best weight:    0.4558

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.138002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.103604 restraints weight = 30097.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.3127 rms_B_bonded: 2.14
r_work: 0.2956 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2830 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.2981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8295  Z= 0.096
  Angle     :  0.473   4.664  11292  Z= 0.247
  Chirality :  0.046   0.405   1246
  Planarity :  0.004   0.034   1460
  Dihedral  :  4.098  36.116   1153
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.48 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 21.28 %
    Favored  : 76.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.95 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.21 (0.25), residues: 1059
  helix: -3.25 (0.54), residues: 55
  sheet:  0.22 (0.24), residues: 460
  loop : -1.46 (0.26), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  72 
 TYR   0.008   0.001   TYR A 352 
 PHE   0.009   0.001   PHE E 116 
 TRP   0.007   0.001   TRP B  47 
 HIS   0.003   0.001   HIS C 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 8285)
  covalent geometry    : angle       0.47188 (11272)
  SS BOND              : bond        0.00256 (   10)
  SS BOND              : angle       0.88488 (   20)
  hydrogen bonds       : bond        0.02576 (  289)
  hydrogen bonds       : angle       5.21736 (  759)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  316 is missing expected H atoms. Skipping.
Residue SER  382 is missing expected H atoms. Skipping.
Residue SER  187 is missing expected H atoms. Skipping.
Residue THR    5 is missing expected H atoms. Skipping.
Residue SER  131 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  136 is missing expected H atoms. Skipping.
Residue VAL  146 is missing expected H atoms. Skipping.
Residue VAL  191 is missing expected H atoms. Skipping.
Residue LEU   18 is missing expected H atoms. Skipping.
Residue THR   21 is missing expected H atoms. Skipping.
Residue LEU   45 is missing expected H atoms. Skipping.
Residue THR  108 is missing expected H atoms. Skipping.
Residue THR  152 is missing expected H atoms. Skipping.
Residue SER  154 is missing expected H atoms. Skipping.
Residue SER  180 is missing expected H atoms. Skipping.
Residue LEU   21 is missing expected H atoms. Skipping.
Residue THR   98 is missing expected H atoms. Skipping.
Residue ILE  118 is missing expected H atoms. Skipping.
Residue SER  160 is missing expected H atoms. Skipping.
Residue THR  165 is missing expected H atoms. Skipping.
Residue VAL  192 is missing expected H atoms. Skipping.
Evaluate side-chains
  120 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  412 PHE cc_start: 0.8468 (OUTLIER) cc_final: 0.7359 (p90)
REVERT: D  146 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7478 (pp)
REVERT: D  150 VAL cc_start: 0.8292 (t) cc_final: 0.8063 (t)
REVERT: D  179 GLN cc_start: 0.7442 (OUTLIER) cc_final: 0.7099 (mp10)
REVERT: E   81 GLU cc_start: 0.8165 (pm20) cc_final: 0.7915 (pm20)
REVERT: E  170 ASP cc_start: 0.7964 (p0) cc_final: 0.7511 (p0)
REVERT: B   11 LEU cc_start: 0.9030 (tp) cc_final: 0.8643 (mt)
REVERT: B   81 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8293 (mtmm)
REVERT: C   82 GLU cc_start: 0.8450 (mp0) cc_final: 0.7918 (pm20)
  outliers start: 19
  outliers final: 11
  residues processed: 116
  average time/residue: 0.1711
  time to fit residues: 28.6042
Evaluate side-chains
  115 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  412 PHE
Chi-restraints excluded: chain A residue  413 THR
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain D residue  104 THR
Chi-restraints excluded: chain D residue  146 LEU
Chi-restraints excluded: chain D residue  179 GLN
Chi-restraints excluded: chain D residue  205 ASN
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain B residue   53 HIS
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue   81 LYS
Chi-restraints excluded: chain B residue  121 SER
Chi-restraints excluded: chain C residue   64 SER
Chi-restraints excluded: chain C residue   71 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 18 optimal weight:    0.5980
   chunk 65 optimal weight:    0.6980
   chunk 92 optimal weight:    1.9990
   chunk 93 optimal weight:    0.5980
   chunk 71 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.135928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.101393 restraints weight = 30301.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.3081 rms_B_bonded: 2.13
r_work: 0.2908 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.2780 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.3058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8295  Z= 0.118
  Angle     :  0.480   4.762  11292  Z= 0.251
  Chirality :  0.046   0.408   1246
  Planarity :  0.004   0.034   1460
  Dihedral  :  4.148  38.807   1153
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.33 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 21.40 %
    Favored  : 76.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.95 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.07 (0.25), residues: 1059
  helix: -3.17 (0.55), residues: 55
  sheet:  0.36 (0.24), residues: 455
  loop : -1.41 (0.26), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  18 
 TYR   0.008   0.001   TYR E  86 
 PHE   0.009   0.001   PHE B  78 
 TRP   0.007   0.001   TRP B  47 
 HIS   0.004   0.001   HIS C 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 8285)
  covalent geometry    : angle       0.47860 (11272)
  SS BOND              : bond        0.00270 (   10)
  SS BOND              : angle       0.98823 (   20)
  hydrogen bonds       : bond        0.02623 (  289)
  hydrogen bonds       : angle       5.22898 (  759)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  316 is missing expected H atoms. Skipping.
Residue SER  382 is missing expected H atoms. Skipping.
Residue SER  187 is missing expected H atoms. Skipping.
Residue THR    5 is missing expected H atoms. Skipping.
Residue SER  131 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  136 is missing expected H atoms. Skipping.
Residue VAL  146 is missing expected H atoms. Skipping.
Residue VAL  191 is missing expected H atoms. Skipping.
Residue LEU   18 is missing expected H atoms. Skipping.
Residue THR   21 is missing expected H atoms. Skipping.
Residue LEU   45 is missing expected H atoms. Skipping.
Residue THR  108 is missing expected H atoms. Skipping.
Residue THR  152 is missing expected H atoms. Skipping.
Residue SER  154 is missing expected H atoms. Skipping.
Residue SER  180 is missing expected H atoms. Skipping.
Residue LEU   21 is missing expected H atoms. Skipping.
Residue THR   98 is missing expected H atoms. Skipping.
Residue ILE  118 is missing expected H atoms. Skipping.
Residue SER  160 is missing expected H atoms. Skipping.
Residue THR  165 is missing expected H atoms. Skipping.
Residue VAL  192 is missing expected H atoms. Skipping.
Evaluate side-chains
  119 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  412 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.7130 (p90)
REVERT: D   16 ARG cc_start: 0.8323 (mmm-85) cc_final: 0.8091 (mtp85)
REVERT: D  146 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7363 (pp)
REVERT: D  150 VAL cc_start: 0.8301 (t) cc_final: 0.8072 (t)
REVERT: E   81 GLU cc_start: 0.8229 (pm20) cc_final: 0.7926 (pm20)
REVERT: E  170 ASP cc_start: 0.8002 (p0) cc_final: 0.7530 (p0)
REVERT: B   11 LEU cc_start: 0.9096 (tp) cc_final: 0.8655 (mt)
REVERT: B   81 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8341 (mtmm)
REVERT: C   82 GLU cc_start: 0.8565 (mp0) cc_final: 0.7909 (pm20)
  outliers start: 17
  outliers final: 10
  residues processed: 118
  average time/residue: 0.1703
  time to fit residues: 28.5668
Evaluate side-chains
  113 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  412 PHE
Chi-restraints excluded: chain A residue  413 THR
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain D residue  104 THR
Chi-restraints excluded: chain D residue  146 LEU
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   33 LEU
Chi-restraints excluded: chain B residue   53 HIS
Chi-restraints excluded: chain B residue   81 LYS
Chi-restraints excluded: chain B residue  121 SER
Chi-restraints excluded: chain C residue   64 SER
Chi-restraints excluded: chain C residue   71 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 88 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
B  56 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.135073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.100343 restraints weight = 30243.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.3079 rms_B_bonded: 2.12
r_work: 0.2900 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2772 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.3197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8295  Z= 0.151
  Angle     :  0.502   5.046  11292  Z= 0.263
  Chirality :  0.046   0.409   1246
  Planarity :  0.004   0.035   1460
  Dihedral  :  4.333  42.038   1153
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.55 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 21.28 %
    Favored  : 76.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.95 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.26), residues: 1059
  helix: -3.16 (0.55), residues: 55
  sheet:  0.41 (0.25), residues: 455
  loop : -1.40 (0.26), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  18 
 TYR   0.009   0.001   TYR B  94 
 PHE   0.010   0.001   PHE E 116 
 TRP   0.009   0.001   TRP B 155 
 HIS   0.005   0.001   HIS B 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 8285)
  covalent geometry    : angle       0.49990 (11272)
  SS BOND              : bond        0.00297 (   10)
  SS BOND              : angle       1.18809 (   20)
  hydrogen bonds       : bond        0.02773 (  289)
  hydrogen bonds       : angle       5.35427 (  759)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  316 is missing expected H atoms. Skipping.
Residue SER  382 is missing expected H atoms. Skipping.
Residue SER  187 is missing expected H atoms. Skipping.
Residue THR    5 is missing expected H atoms. Skipping.
Residue SER  131 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  136 is missing expected H atoms. Skipping.
Residue VAL  146 is missing expected H atoms. Skipping.
Residue VAL  191 is missing expected H atoms. Skipping.
Residue LEU   18 is missing expected H atoms. Skipping.
Residue THR   21 is missing expected H atoms. Skipping.
Residue LEU   45 is missing expected H atoms. Skipping.
Residue THR  108 is missing expected H atoms. Skipping.
Residue THR  152 is missing expected H atoms. Skipping.
Residue SER  154 is missing expected H atoms. Skipping.
Residue SER  180 is missing expected H atoms. Skipping.
Residue LEU   21 is missing expected H atoms. Skipping.
Residue THR   98 is missing expected H atoms. Skipping.
Residue ILE  118 is missing expected H atoms. Skipping.
Residue SER  160 is missing expected H atoms. Skipping.
Residue THR  165 is missing expected H atoms. Skipping.
Residue VAL  192 is missing expected H atoms. Skipping.
Evaluate side-chains
  117 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  412 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.7545 (p90)
REVERT: D   16 ARG cc_start: 0.8305 (mmm-85) cc_final: 0.8079 (mtp85)
REVERT: E   81 GLU cc_start: 0.8189 (pm20) cc_final: 0.7947 (pm20)
REVERT: E  170 ASP cc_start: 0.8077 (p0) cc_final: 0.7640 (p0)
REVERT: B   11 LEU cc_start: 0.8994 (tp) cc_final: 0.8593 (mt)
REVERT: B   81 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8332 (mtmm)
REVERT: C   82 GLU cc_start: 0.8513 (mp0) cc_final: 0.7955 (pm20)
  outliers start: 18
  outliers final: 14
  residues processed: 116
  average time/residue: 0.1608
  time to fit residues: 27.2407
Evaluate side-chains
  114 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  412 PHE
Chi-restraints excluded: chain A residue  413 THR
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain D residue   96 CYS
Chi-restraints excluded: chain D residue  104 THR
Chi-restraints excluded: chain D residue  149 LEU
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain E residue   33 LEU
Chi-restraints excluded: chain B residue   53 HIS
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue   81 LYS
Chi-restraints excluded: chain B residue  121 SER
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain C residue   27 GLN
Chi-restraints excluded: chain C residue   64 SER
Chi-restraints excluded: chain C residue   71 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 94 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9980
   chunk 41 optimal weight:    0.3980
   chunk 48 optimal weight:    0.6980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.142984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.106937 restraints weight = 29542.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.3106 rms_B_bonded: 2.16
r_work: 0.2956 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2822 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.2822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.3267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8295  Z= 0.120
  Angle     :  0.488   4.753  11292  Z= 0.255
  Chirality :  0.046   0.407   1246
  Planarity :  0.004   0.035   1460
  Dihedral  :  4.236  39.504   1153
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.85 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 21.51 %
    Favored  : 76.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.95 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.92 (0.26), residues: 1059
  helix: -3.11 (0.56), residues: 55
  sheet:  0.47 (0.25), residues: 455
  loop : -1.31 (0.26), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  18 
 TYR   0.007   0.001   TYR A 352 
 PHE   0.011   0.001   PHE E 116 
 TRP   0.008   0.001   TRP B  47 
 HIS   0.003   0.001   HIS C 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 8285)
  covalent geometry    : angle       0.48680 (11272)
  SS BOND              : bond        0.00268 (   10)
  SS BOND              : angle       1.03820 (   20)
  hydrogen bonds       : bond        0.02652 (  289)
  hydrogen bonds       : angle       5.28855 (  759)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  316 is missing expected H atoms. Skipping.
Residue SER  382 is missing expected H atoms. Skipping.
Residue SER  187 is missing expected H atoms. Skipping.
Residue THR    5 is missing expected H atoms. Skipping.
Residue SER  131 is missing expected H atoms. Skipping.
Residue VAL  132 is missing expected H atoms. Skipping.
Residue LEU  136 is missing expected H atoms. Skipping.
Residue VAL  146 is missing expected H atoms. Skipping.
Residue VAL  191 is missing expected H atoms. Skipping.
Residue LEU   18 is missing expected H atoms. Skipping.
Residue THR   21 is missing expected H atoms. Skipping.
Residue LEU   45 is missing expected H atoms. Skipping.
Residue THR  108 is missing expected H atoms. Skipping.
Residue THR  152 is missing expected H atoms. Skipping.
Residue SER  154 is missing expected H atoms. Skipping.
Residue SER  180 is missing expected H atoms. Skipping.
Residue LEU   21 is missing expected H atoms. Skipping.
Residue THR   98 is missing expected H atoms. Skipping.
Residue ILE  118 is missing expected H atoms. Skipping.
Residue SER  160 is missing expected H atoms. Skipping.
Residue THR  165 is missing expected H atoms. Skipping.
Residue VAL  192 is missing expected H atoms. Skipping.
Evaluate side-chains
  120 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  412 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.7243 (p90)
REVERT: D   16 ARG cc_start: 0.8284 (mmm-85) cc_final: 0.8042 (mtp85)
REVERT: E   81 GLU cc_start: 0.8237 (pm20) cc_final: 0.7939 (pm20)
REVERT: E  170 ASP cc_start: 0.8055 (p0) cc_final: 0.7596 (p0)
REVERT: B   11 LEU cc_start: 0.9097 (tp) cc_final: 0.8649 (mt)
REVERT: B   81 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8357 (mtmm)
REVERT: C   82 GLU cc_start: 0.8621 (mp0) cc_final: 0.7952 (pm20)
  outliers start: 16
  outliers final: 13
  residues processed: 118
  average time/residue: 0.1556
  time to fit residues: 27.0304
Evaluate side-chains
  115 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  412 PHE
Chi-restraints excluded: chain A residue  413 THR
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain D residue   96 CYS
Chi-restraints excluded: chain D residue  104 THR
Chi-restraints excluded: chain D residue  149 LEU
Chi-restraints excluded: chain E residue   11 VAL
Chi-restraints excluded: chain E residue   33 LEU
Chi-restraints excluded: chain B residue   53 HIS
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue   81 LYS
Chi-restraints excluded: chain B residue  121 SER
Chi-restraints excluded: chain C residue   27 GLN
Chi-restraints excluded: chain C residue   64 SER
Chi-restraints excluded: chain C residue   71 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 102 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 47 optimal weight:    4.9990
   chunk 73 optimal weight:    0.9990
   chunk 81 optimal weight:    0.7980
   chunk 83 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9980
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.135292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.100784 restraints weight = 30456.936|
|-----------------------------------------------------------------------------|
r_work (start): 0.3074 rms_B_bonded: 2.10
r_work: 0.2895 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2767 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.2767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.3326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8295  Z= 0.138
  Angle     :  0.511   9.072  11292  Z= 0.268
  Chirality :  0.046   0.410   1246
  Planarity :  0.004   0.035   1460
  Dihedral  :  4.300  39.517   1153
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.99 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 21.40 %
    Favored  : 76.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.95 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.89 (0.26), residues: 1059
  helix: -3.08 (0.56), residues: 55
  sheet:  0.49 (0.25), residues: 453
  loop : -1.28 (0.26), residues: 551

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  18 
 TYR   0.010   0.001   TYR A 406 
 PHE   0.009   0.001   PHE E 116 
 TRP   0.009   0.001   TRP B 155 
 HIS   0.003   0.001   HIS B 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 8285)
  covalent geometry    : angle       0.50196 (11272)
  SS BOND              : bond        0.00295 (   10)
  SS BOND              : angle       2.37248 (   20)
  hydrogen bonds       : bond        0.02752 (  289)
  hydrogen bonds       : angle       5.39313 (  759)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4548.27 seconds
wall clock time: 77 minutes 48.52 seconds (4668.52 seconds total)