Starting phenix.real_space_refine
on Thu Mar 13 19:20:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dzj_27801/03_2025/8dzj_27801.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dzj_27801/03_2025/8dzj_27801.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dzj_27801/03_2025/8dzj_27801.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dzj_27801/03_2025/8dzj_27801.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dzj_27801/03_2025/8dzj_27801.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dzj_27801/03_2025/8dzj_27801.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P     190      5.49       5
     S      21      5.16       5
     C    4988      2.51       5
     N    1635      2.21       5
     O    2195      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9030
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3369
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 416, 3369
          Classifications: {'peptide': 416}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 405}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 1622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 197, 1622
          Classifications: {'peptide': 197}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 192}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "C"
      Number of atoms: 560
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 560
          Classifications: {'DNA': 27}
          Link IDs: {'rna3p': 26}
    Chain: "D"
      Number of atoms: 206
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 206
          Classifications: {'DNA': 10}
          Link IDs: {'rna3p': 9}
    Chain: "E"
      Number of atoms: 3272
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 153, 3272
          Classifications: {'RNA': 153}
          Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 5, 'rna3p_pur': 75, 'rna3p_pyr': 62}
          Link IDs: {'rna2p': 16, 'rna3p': 136}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2994  SG  CYS A 372      44.439  13.422  45.939  1.00 30.07           S
  ATOM   3015  SG  CYS A 375      42.544  10.078  46.726  1.00 35.03           S
  ATOM   3132  SG  CYS A 391      45.670  10.363  47.236  1.00 37.27           S
  ATOM   3154  SG  CYS A 394      44.416   9.788  43.268  1.00 37.08           S

  Time building chain proxies: 8.47, per 1000 atoms: 0.94
  Number of scatterers: 9030
  At special positions: 0
  Unit cell: (85.2, 116.085, 137.385, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     S      21     16.00
     P     190     15.00
     O    2195      8.00
     N    1635      7.00
     C    4988      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.23
  Conformation dependent library (CDL) restraints added in 899.6 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 501 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 391 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 375 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 394 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 372 "
      Number of angles added : 6


  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1148

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 5 sheets defined
      50.6% alpha, 20.1% beta
      69 base pairs and 112 stacking pairs defined.
    Time for finding SS restraints: 4.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 57
    Processing helix  chain 'A' and resid 61 through 66
    Processing helix  chain 'A' and resid 70 through 80
      removed outlier: 3.736A  pdb=" N   TYR A  74 " --> pdb=" O   ASN A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 105
      removed outlier: 3.517A  pdb=" N   TYR A 105 " --> pdb=" O   ARG A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 111
    Processing helix  chain 'A' and resid 128 through 130
      No H-bonds generated for 'chain 'A' and resid 128 through 130'
    Processing helix  chain 'A' and resid 150 through 157
    Processing helix  chain 'A' and resid 170 through 182
    Processing helix  chain 'A' and resid 247 through 270
      removed outlier: 3.814A  pdb=" N   LYS A 269 " --> pdb=" O   LEU A 265 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   TYR A 270 " --> pdb=" O   ARG A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 278
      removed outlier: 4.141A  pdb=" N   HIS A 278 " --> pdb=" O   ALA A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 316
    Processing helix  chain 'A' and resid 325 through 330
      removed outlier: 4.120A  pdb=" N   ILE A 329 " --> pdb=" O   ASP A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 357
    Processing helix  chain 'A' and resid 400 through 410
    Processing helix  chain 'A' and resid 412 through 422
    Processing helix  chain 'B' and resid 16 through 46
    Processing helix  chain 'B' and resid 70 through 80
      removed outlier: 3.525A  pdb=" N   TYR B  74 " --> pdb=" O   ASN B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 87 through 111
      removed outlier: 5.481A  pdb=" N   LYS B 107 " --> pdb=" O   LYS B 103 " (cutoff:3.500A)
      removed outlier: 5.797A  pdb=" N   GLU B 108 " --> pdb=" O   ALA B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 128 through 130
      No H-bonds generated for 'chain 'B' and resid 128 through 130'
    Processing helix  chain 'B' and resid 150 through 158
    Processing helix  chain 'B' and resid 171 through 183
    Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 127
      removed outlier: 4.550A  pdb=" N   SER A 206 " --> pdb=" O   SER A 188 " (cutoff:3.500A)
      removed outlier: 4.806A  pdb=" N   SER A 190 " --> pdb=" O   ASN A 204 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   ASN A 204 " --> pdb=" O   SER A 190 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   ILE A 192 " --> pdb=" O   TYR A 202 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   TYR A 202 " --> pdb=" O   ILE A 192 " (cutoff:3.500A)
      removed outlier: 4.579A  pdb=" N   HIS A 194 " --> pdb=" O   LYS A 200 " (cutoff:3.500A)
      removed outlier: 6.253A  pdb=" N   LYS A 200 " --> pdb=" O   HIS A 194 " (cutoff:3.500A)
      removed outlier: 4.868A  pdb=" N   TRP A 201 " --> pdb=" O   ILE A   9 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   ILE A   9 " --> pdb=" O   ILE A 168 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   ILE A 168 " --> pdb=" O   ILE A   9 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   LYS A  11 " --> pdb=" O   ILE A 166 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   SER A 164 " --> pdb=" O   LEU A  13 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   TYR A 142 " --> pdb=" O   ILE A 167 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 242 through 245
      removed outlier: 6.034A  pdb=" N   MET A 222 " --> pdb=" O   GLN A 322 " (cutoff:3.500A)
      removed outlier: 8.318A  pdb=" N   GLU A 324 " --> pdb=" O   MET A 222 " (cutoff:3.500A)
      removed outlier: 8.798A  pdb=" N   ILE A 224 " --> pdb=" O   GLU A 324 " (cutoff:3.500A)
      removed outlier: 6.128A  pdb=" N   ILE A 321 " --> pdb=" O   ILE A 361 " (cutoff:3.500A)
      removed outlier: 7.314A  pdb=" N   ILE A 363 " --> pdb=" O   ILE A 321 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   MET A 323 " --> pdb=" O   ILE A 363 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 388 through 391
    Processing sheet with id=AA4, first strand: chain 'B' and resid 125 through 127
      removed outlier: 5.064A  pdb=" N   TRP B 201 " --> pdb=" O   ILE B   9 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   LYS B  11 " --> pdb=" O   ILE B 166 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   TYR B 142 " --> pdb=" O   ILE B 167 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 125 through 127

    295 hydrogen bonds defined for protein.
    846 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      174 hydrogen bonds
      324 hydrogen bond angles
      0 basepair planarities
      69 basepair parallelities
      112 stacking parallelities
  Total time for adding SS restraints: 7.24

  Time building geometry restraints manager: 3.09 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1711
        1.33 -     1.45: 3255
        1.45 -     1.57: 4226
        1.57 -     1.69: 376
        1.69 -     1.81: 37
  Bond restraints: 9605
  Sorted by residual:
  bond pdb=" N   ILE A 332 "
       pdb=" CA  ILE A 332 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.038 1.21e-02 6.83e+03 9.61e+00
  bond pdb=" N   ILE A 329 "
       pdb=" CA  ILE A 329 "
    ideal  model  delta    sigma   weight residual
    1.460  1.497 -0.037 1.26e-02 6.30e+03 8.65e+00
  bond pdb=" N   ILE A 250 "
       pdb=" CA  ILE A 250 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.17e-02 7.31e+03 8.03e+00
  bond pdb=" N   VAL A 257 "
       pdb=" CA  VAL A 257 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.036 1.30e-02 5.92e+03 7.77e+00
  bond pdb=" N   GLU A 251 "
       pdb=" CA  GLU A 251 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.21e-02 6.83e+03 6.70e+00
  ... (remaining 9600 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.41: 13336
        1.41 -     2.81: 448
        2.81 -     4.22: 65
        4.22 -     5.63: 13
        5.63 -     7.04: 2
  Bond angle restraints: 13864
  Sorted by residual:
  angle pdb=" C   ARG A 280 "
        pdb=" N   ASP A 281 "
        pdb=" CA  ASP A 281 "
      ideal   model   delta    sigma   weight residual
     121.54  128.58   -7.04 1.91e+00 2.74e-01 1.36e+01
  angle pdb=" CA  ILE A 250 "
        pdb=" C   ILE A 250 "
        pdb=" O   ILE A 250 "
      ideal   model   delta    sigma   weight residual
     121.17  117.40    3.77 1.06e+00 8.90e-01 1.27e+01
  angle pdb=" CA  ILE A 332 "
        pdb=" C   ILE A 332 "
        pdb=" O   ILE A 332 "
      ideal   model   delta    sigma   weight residual
     120.96  117.30    3.66 1.19e+00 7.06e-01 9.46e+00
  angle pdb=" CA  GLN A 256 "
        pdb=" C   GLN A 256 "
        pdb=" O   GLN A 256 "
      ideal   model   delta    sigma   weight residual
     120.82  117.79    3.03 1.05e+00 9.07e-01 8.35e+00
  angle pdb=" CA  ASP A 331 "
        pdb=" C   ASP A 331 "
        pdb=" O   ASP A 331 "
      ideal   model   delta    sigma   weight residual
     120.82  117.80    3.02 1.05e+00 9.07e-01 8.26e+00
  ... (remaining 13859 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.54: 4904
       21.54 -    43.09: 522
       43.09 -    64.63: 356
       64.63 -    86.17: 45
       86.17 -   107.71: 6
  Dihedral angle restraints: 5833
    sinusoidal: 4038
      harmonic: 1795
  Sorted by residual:
  dihedral pdb=" CA  LYS A 282 "
           pdb=" C   LYS A 282 "
           pdb=" N   ARG A 283 "
           pdb=" CA  ARG A 283 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.50  -21.50     0      5.00e+00 4.00e-02 1.85e+01
  dihedral pdb=" O4'   C E  94 "
           pdb=" C1'   C E  94 "
           pdb=" N1    C E  94 "
           pdb=" C2    C E  94 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00  -65.32  -62.68     1      1.70e+01 3.46e-03 1.80e+01
  dihedral pdb=" O4'   A E 106 "
           pdb=" C1'   A E 106 "
           pdb=" N9    A E 106 "
           pdb=" C4    A E 106 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -78.00  -16.27  -61.73     1      1.70e+01 3.46e-03 1.75e+01
  ... (remaining 5830 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 1465
       0.060 -    0.119: 149
       0.119 -    0.179: 25
       0.179 -    0.239: 2
       0.239 -    0.298: 1
  Chirality restraints: 1642
  Sorted by residual:
  chirality pdb=" P     G E  34 "
            pdb=" OP1   G E  34 "
            pdb=" OP2   G E  34 "
            pdb=" O5'   G E  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.71   -0.30 2.00e-01 2.50e+01 2.22e+00
  chirality pdb=" CA  LEU A 337 "
            pdb=" N   LEU A 337 "
            pdb=" C   LEU A 337 "
            pdb=" CB  LEU A 337 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.15e+00
  chirality pdb=" C1'   A E  91 "
            pdb=" O4'   A E  91 "
            pdb=" C2'   A E  91 "
            pdb=" N9    A E  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.27    0.19 2.00e-01 2.50e+01 9.16e-01
  ... (remaining 1639 not shown)

  Planarity restraints: 1064
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 233 "    0.015 2.00e-02 2.50e+03   1.53e-02 4.67e+00
        pdb=" CG  TYR A 233 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 233 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 233 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 233 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 233 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 233 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 233 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G E  31 "   -0.026 2.00e-02 2.50e+03   1.20e-02 4.30e+00
        pdb=" N9    G E  31 "    0.029 2.00e-02 2.50e+03
        pdb=" C8    G E  31 "    0.004 2.00e-02 2.50e+03
        pdb=" N7    G E  31 "    0.002 2.00e-02 2.50e+03
        pdb=" C5    G E  31 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    G E  31 "   -0.003 2.00e-02 2.50e+03
        pdb=" O6    G E  31 "   -0.005 2.00e-02 2.50e+03
        pdb=" N1    G E  31 "   -0.006 2.00e-02 2.50e+03
        pdb=" C2    G E  31 "   -0.003 2.00e-02 2.50e+03
        pdb=" N2    G E  31 "    0.010 2.00e-02 2.50e+03
        pdb=" N3    G E  31 "   -0.000 2.00e-02 2.50e+03
        pdb=" C4    G E  31 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A E  91 "    0.026 2.00e-02 2.50e+03   1.12e-02 3.48e+00
        pdb=" N9    A E  91 "   -0.024 2.00e-02 2.50e+03
        pdb=" C8    A E  91 "   -0.005 2.00e-02 2.50e+03
        pdb=" N7    A E  91 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    A E  91 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    A E  91 "    0.003 2.00e-02 2.50e+03
        pdb=" N6    A E  91 "    0.008 2.00e-02 2.50e+03
        pdb=" N1    A E  91 "    0.001 2.00e-02 2.50e+03
        pdb=" C2    A E  91 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3    A E  91 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    A E  91 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 1061 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1068
        2.75 -     3.29: 8440
        3.29 -     3.82: 17829
        3.82 -     4.36: 21444
        4.36 -     4.90: 31208
  Nonbonded interactions: 79989
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 288 "
            pdb=" NH2 ARG A 291 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" NH1 ARG A 291 "
            pdb=" OP1  DC C  21 "
     model   vdw
     2.211 3.120
  nonbonded pdb=" O6    G E  36 "
            pdb=" O4    U E  62 "
     model   vdw
     2.229 2.432
  nonbonded pdb=" O2'   C E 174 "
            pdb=" O4'   U E 175 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" O   TYR B  84 "
            pdb=" OG  SER B 150 "
     model   vdw
     2.255 3.040
  ... (remaining 79984 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:             110.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     38.360
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.050
  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:80.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  229.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6890
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   0.038   9605  Z= 0.220
  Angle     :  0.604   7.037  13864  Z= 0.359
  Chirality :  0.039   0.298   1642
  Planarity :  0.004   0.038   1064
  Dihedral  : 21.353 107.713   4685
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 12.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  0.19 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.33), residues: 605
  helix:  1.65 (0.30), residues: 298
  sheet:  0.21 (0.43), residues: 130
  loop : -0.75 (0.43), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  43 
 HIS   0.012   0.001   HIS A 303 
 PHE   0.008   0.001   PHE A 336 
 TYR   0.036   0.002   TYR A 233 
 ARG   0.012   0.001   ARG A 291 

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

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

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 88
  time to evaluate  : 0.979 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 89
  average time/residue: 1.7701
  time to fit residues: 168.1680
Evaluate side-chains
  47 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 46
  time to evaluate  : 1.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  326 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    9.9990
   chunk 59 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0270
   chunk 20 optimal weight:    0.5980
   chunk 39 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 37 optimal weight:   20.0000
   chunk 45 optimal weight:    4.9990
   chunk 70 optimal weight:    8.9990
   overall best weight:    0.8842

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

Flipped N/Q/H residues before XYZ refinement:
A 322 GLN
B  26 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.090965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.065318 restraints weight = 26371.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.3429 rms_B_bonded: 2.26
r_work: 0.3275 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.1481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9605  Z= 0.177
  Angle     :  0.549   6.546  13864  Z= 0.296
  Chirality :  0.035   0.189   1642
  Planarity :  0.005   0.040   1064
  Dihedral  : 22.491 106.258   3433
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  :  9.42 %
    Favored  : 89.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.33), residues: 605
  helix:  2.28 (0.29), residues: 304
  sheet:  0.19 (0.41), residues: 134
  loop : -0.74 (0.44), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  45 
 HIS   0.006   0.001   HIS A 303 
 PHE   0.008   0.001   PHE A 389 
 TYR   0.024   0.001   TYR A 351 
 ARG   0.011   0.001   ARG A 242 

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

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

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 49
  time to evaluate  : 0.758 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7736 (mt-10)
REVERT: A  222 MET cc_start: 0.8300 (ttm) cc_final: 0.7925 (ttt)
REVERT: A  270 TYR cc_start: 0.4550 (t80) cc_final: 0.4177 (m-80)
REVERT: A  288 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8668 (mm-30)
REVERT: A  292 ASP cc_start: 0.8822 (m-30) cc_final: 0.8502 (m-30)
REVERT: B  155 GLN cc_start: 0.8926 (mm110) cc_final: 0.8706 (mm-40)
REVERT: B  156 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8490 (tm-30)
REVERT: B  177 MET cc_start: 0.8432 (mmm) cc_final: 0.8209 (mmm)
  outliers start: 7
  outliers final: 6
  residues processed: 54
  average time/residue: 1.1571
  time to fit residues: 67.6550
Evaluate side-chains
  48 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.654 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   66 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 35 optimal weight:    8.9990
   chunk 76 optimal weight:    5.9990
   chunk 63 optimal weight:    5.9990
   chunk 0 optimal weight:    3.9990
   chunk 14 optimal weight:    5.9990
   chunk 50 optimal weight:    2.9990
   chunk 46 optimal weight:    9.9990
   chunk 19 optimal weight:    5.9990
   chunk 18 optimal weight:    0.7980
   chunk 7 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   overall best weight:    1.9184

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

Flipped N/Q/H residues before XYZ refinement:
A  56 HIS
A 346 GLN
A 366 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.088112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.062154 restraints weight = 27082.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.3357 rms_B_bonded: 2.35
r_work: 0.3199 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.2066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9605  Z= 0.262
  Angle     :  0.584   9.006  13864  Z= 0.312
  Chirality :  0.037   0.187   1642
  Planarity :  0.004   0.043   1064
  Dihedral  : 22.524 105.814   3433
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 11.30 %
    Favored  : 87.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.33), residues: 605
  helix:  2.38 (0.29), residues: 304
  sheet:  0.05 (0.41), residues: 132
  loop : -0.70 (0.45), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B  45 
 HIS   0.007   0.001   HIS A 303 
 PHE   0.010   0.002   PHE A 253 
 TYR   0.021   0.002   TYR A 351 
 ARG   0.007   0.001   ARG A 242 

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

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

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 45
  time to evaluate  : 0.616 
Fit side-chains
   revert: symmetry clash
REVERT: A  222 MET cc_start: 0.8525 (ttm) cc_final: 0.8055 (ttt)
REVERT: A  288 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8626 (mm-30)
REVERT: A  292 ASP cc_start: 0.8804 (m-30) cc_final: 0.8587 (m-30)
REVERT: B   26 GLN cc_start: 0.8141 (mm110) cc_final: 0.7808 (mm-40)
REVERT: B  130 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8517 (mm-30)
REVERT: B  156 GLU cc_start: 0.9018 (tm-30) cc_final: 0.8716 (tm-30)
REVERT: B  177 MET cc_start: 0.8580 (mmm) cc_final: 0.8302 (mmm)
  outliers start: 9
  outliers final: 4
  residues processed: 51
  average time/residue: 1.2294
  time to fit residues: 67.4391
Evaluate side-chains
  45 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 41
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   66 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 48 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 57 optimal weight:    8.9990
   chunk 51 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0670
   chunk 45 optimal weight:    3.9990
   chunk 41 optimal weight:    6.9990
   chunk 55 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    1.8124

-------------------------------------------------------------------------------
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 = 0.3968 r_free = 0.3968 target = 0.087869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.062225 restraints weight = 26835.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.3357 rms_B_bonded: 2.33
r_work: 0.3199 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.2344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   9605  Z= 0.243
  Angle     :  0.574   8.659  13864  Z= 0.307
  Chirality :  0.037   0.192   1642
  Planarity :  0.004   0.045   1064
  Dihedral  : 22.440 107.008   3431
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 11.49 %
    Favored  : 86.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.33), residues: 605
  helix:  2.39 (0.29), residues: 304
  sheet: -0.08 (0.40), residues: 134
  loop : -0.73 (0.45), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  43 
 HIS   0.006   0.001   HIS A 303 
 PHE   0.017   0.002   PHE A 253 
 TYR   0.021   0.001   TYR A 351 
 ARG   0.005   0.001   ARG A 242 

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

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

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.692 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7785 (mt-10)
REVERT: A  222 MET cc_start: 0.8462 (ttm) cc_final: 0.8051 (ttt)
REVERT: A  288 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8432 (tp30)
REVERT: A  292 ASP cc_start: 0.8898 (m-30) cc_final: 0.8507 (m-30)
REVERT: B   26 GLN cc_start: 0.8157 (mm110) cc_final: 0.7679 (mm-40)
REVERT: B  130 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8613 (mm-30)
REVERT: B  156 GLU cc_start: 0.9063 (tm-30) cc_final: 0.8561 (tm-30)
REVERT: B  177 MET cc_start: 0.8596 (mmm) cc_final: 0.8389 (mmm)
  outliers start: 9
  outliers final: 6
  residues processed: 50
  average time/residue: 1.1640
  time to fit residues: 63.0513
Evaluate side-chains
  46 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain B residue    8 GLU
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   66 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 46 optimal weight:    9.9990
   chunk 74 optimal weight:    8.9990
   chunk 7 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   chunk 60 optimal weight:   10.0000
   chunk 21 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 77 optimal weight:    8.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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 = 0.3991 r_free = 0.3991 target = 0.088889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.063346 restraints weight = 27011.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 2.31
r_work: 0.3231 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.2518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9605  Z= 0.184
  Angle     :  0.548   9.687  13864  Z= 0.292
  Chirality :  0.035   0.186   1642
  Planarity :  0.004   0.040   1064
  Dihedral  : 22.345 107.298   3431
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 12.99 %
    Favored  : 85.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.34), residues: 605
  helix:  2.52 (0.29), residues: 303
  sheet: -0.00 (0.40), residues: 132
  loop : -0.63 (0.45), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  45 
 HIS   0.004   0.001   HIS A 303 
 PHE   0.020   0.002   PHE A 253 
 TYR   0.020   0.001   TYR A 351 
 ARG   0.006   0.000   ARG A 291 

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

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

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.684 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7773 (mt-10)
REVERT: A  222 MET cc_start: 0.8310 (ttm) cc_final: 0.7972 (ttm)
REVERT: A  288 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8369 (tp30)
REVERT: A  292 ASP cc_start: 0.8895 (m-30) cc_final: 0.8499 (m-30)
REVERT: B   26 GLN cc_start: 0.8157 (mm110) cc_final: 0.7418 (mm-40)
REVERT: B   30 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7778 (mp0)
REVERT: B  130 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8628 (mm-30)
REVERT: B  156 GLU cc_start: 0.8977 (tm-30) cc_final: 0.8557 (tm-30)
REVERT: B  177 MET cc_start: 0.8600 (mmm) cc_final: 0.8388 (mmm)
  outliers start: 8
  outliers final: 5
  residues processed: 49
  average time/residue: 1.2125
  time to fit residues: 63.8851
Evaluate side-chains
  46 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 41
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  238 HIS
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   66 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 45 optimal weight:    5.9990
   chunk 72 optimal weight:    8.9990
   chunk 27 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 13 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   chunk 71 optimal weight:    7.9990
   chunk 2 optimal weight:    0.0670
   overall best weight:    1.2124

-------------------------------------------------------------------------------
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 = 0.3989 r_free = 0.3989 target = 0.088828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.063161 restraints weight = 27039.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.3382 rms_B_bonded: 2.33
r_work: 0.3228 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.2637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9605  Z= 0.194
  Angle     :  0.555  13.560  13864  Z= 0.294
  Chirality :  0.035   0.182   1642
  Planarity :  0.004   0.039   1064
  Dihedral  : 22.322 107.008   3431
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 13.18 %
    Favored  : 85.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.34), residues: 605
  helix:  2.48 (0.29), residues: 305
  sheet:  0.04 (0.40), residues: 132
  loop : -0.61 (0.46), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  45 
 HIS   0.003   0.001   HIS A 303 
 PHE   0.025   0.002   PHE A 253 
 TYR   0.019   0.001   TYR A 351 
 ARG   0.005   0.000   ARG A 291 

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

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

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.672 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7748 (mt-10)
REVERT: A  193 ILE cc_start: 0.9089 (pt) cc_final: 0.8886 (pt)
REVERT: A  222 MET cc_start: 0.8328 (ttm) cc_final: 0.8014 (ttm)
REVERT: A  288 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8304 (tp30)
REVERT: A  292 ASP cc_start: 0.8897 (m-30) cc_final: 0.8501 (m-30)
REVERT: B   26 GLN cc_start: 0.8184 (mm110) cc_final: 0.7671 (mm-40)
REVERT: B  130 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8648 (mm-30)
REVERT: B  156 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8555 (tm-30)
REVERT: B  177 MET cc_start: 0.8559 (mmm) cc_final: 0.8347 (mmm)
  outliers start: 8
  outliers final: 6
  residues processed: 50
  average time/residue: 1.2012
  time to fit residues: 64.6424
Evaluate side-chains
  49 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  238 HIS
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   66 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 63 optimal weight:    6.9990
   chunk 67 optimal weight:    9.9990
   chunk 23 optimal weight:    5.9990
   chunk 0 optimal weight:    4.9990
   chunk 54 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   chunk 29 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 27 optimal weight:    0.1980
   overall best weight:    2.2388

-------------------------------------------------------------------------------
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 = 0.3950 r_free = 0.3950 target = 0.086826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.061322 restraints weight = 27599.802|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 2.38
r_work: 0.3180 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.2823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   9605  Z= 0.290
  Angle     :  0.615  14.591  13864  Z= 0.323
  Chirality :  0.037   0.192   1642
  Planarity :  0.004   0.046   1064
  Dihedral  : 22.465 106.111   3431
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 13.56 %
    Favored  : 84.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.33), residues: 605
  helix:  2.39 (0.29), residues: 301
  sheet: -0.08 (0.40), residues: 130
  loop : -0.73 (0.45), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B  43 
 HIS   0.004   0.002   HIS A 303 
 PHE   0.028   0.002   PHE A 253 
 TYR   0.019   0.002   TYR A 351 
 ARG   0.005   0.000   ARG B 136 

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

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

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7804 (mt-10)
REVERT: A  222 MET cc_start: 0.8477 (ttm) cc_final: 0.8119 (ttm)
REVERT: A  288 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8390 (tp30)
REVERT: A  292 ASP cc_start: 0.8921 (m-30) cc_final: 0.8603 (m-30)
REVERT: B   26 GLN cc_start: 0.8198 (mm110) cc_final: 0.7669 (mm-40)
REVERT: B  130 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8647 (mm-30)
REVERT: B  156 GLU cc_start: 0.9004 (tm-30) cc_final: 0.8592 (tm-30)
REVERT: B  177 MET cc_start: 0.8584 (mmm) cc_final: 0.8364 (mmm)
  outliers start: 8
  outliers final: 6
  residues processed: 49
  average time/residue: 1.2270
  time to fit residues: 64.9600
Evaluate side-chains
  43 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  238 HIS
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   66 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 64 optimal weight:    6.9990
   chunk 56 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   chunk 76 optimal weight:    4.9990
   chunk 35 optimal weight:    8.9990
   chunk 43 optimal weight:    2.9990
   chunk 26 optimal weight:   10.0000
   chunk 38 optimal weight:    0.4980
   chunk 45 optimal weight:    4.9990
   overall best weight:    2.8988

-------------------------------------------------------------------------------
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 = 0.3920 r_free = 0.3920 target = 0.085114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.059868 restraints weight = 28167.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 2.42
r_work: 0.3145 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.3156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   9605  Z= 0.361
  Angle     :  0.678  14.838  13864  Z= 0.355
  Chirality :  0.041   0.250   1642
  Planarity :  0.005   0.058   1064
  Dihedral  : 22.619 107.105   3431
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 12.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 13.75 %
    Favored  : 84.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.33), residues: 605
  helix:  2.11 (0.30), residues: 302
  sheet: -0.11 (0.40), residues: 129
  loop : -0.80 (0.44), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  43 
 HIS   0.006   0.002   HIS A 303 
 PHE   0.034   0.002   PHE A 253 
 TYR   0.018   0.002   TYR A 351 
 ARG   0.004   0.001   ARG B 136 

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

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

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 41
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7793 (mt-10)
REVERT: A  222 MET cc_start: 0.8553 (ttm) cc_final: 0.8147 (ttm)
REVERT: A  288 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8344 (tp30)
REVERT: A  292 ASP cc_start: 0.8900 (m-30) cc_final: 0.8529 (m-30)
REVERT: B   26 GLN cc_start: 0.8206 (mm110) cc_final: 0.7787 (mm-40)
REVERT: B  156 GLU cc_start: 0.9006 (tm-30) cc_final: 0.8520 (tm-30)
REVERT: B  177 MET cc_start: 0.8665 (mmm) cc_final: 0.8433 (mmm)
  outliers start: 10
  outliers final: 6
  residues processed: 49
  average time/residue: 1.3869
  time to fit residues: 72.7475
Evaluate side-chains
  46 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  238 HIS
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain B residue    8 GLU
Chi-restraints excluded: chain B residue   66 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   chunk 69 optimal weight:    8.9990
   chunk 9 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   chunk 65 optimal weight:    6.9990
   chunk 53 optimal weight:    6.9990
   chunk 23 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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 = 0.3973 r_free = 0.3973 target = 0.087776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.062626 restraints weight = 27479.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 2.33
r_work: 0.3213 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.3175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9605  Z= 0.201
  Angle     :  0.597  12.820  13864  Z= 0.312
  Chirality :  0.036   0.202   1642
  Planarity :  0.004   0.039   1064
  Dihedral  : 22.297 109.288   3431
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 14.69 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.34), residues: 605
  helix:  2.41 (0.30), residues: 301
  sheet: -0.12 (0.41), residues: 131
  loop : -0.63 (0.46), residues: 173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  45 
 HIS   0.003   0.001   HIS A 278 
 PHE   0.034   0.002   PHE A 253 
 TYR   0.020   0.001   TYR A 351 
 ARG   0.003   0.000   ARG A 242 

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

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

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 47
  time to evaluate  : 0.685 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7761 (mt-10)
REVERT: A  222 MET cc_start: 0.8325 (ttm) cc_final: 0.7985 (ttm)
REVERT: A  288 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8356 (tp30)
REVERT: A  292 ASP cc_start: 0.8929 (m-30) cc_final: 0.8605 (m-30)
REVERT: B   26 GLN cc_start: 0.8144 (mm110) cc_final: 0.7411 (mm-40)
REVERT: B   30 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7802 (mp0)
REVERT: B  156 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8713 (tm-30)
REVERT: B  177 MET cc_start: 0.8578 (mmm) cc_final: 0.8362 (mmm)
  outliers start: 8
  outliers final: 7
  residues processed: 52
  average time/residue: 1.4088
  time to fit residues: 78.4714
Evaluate side-chains
  49 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 42
  time to evaluate  : 0.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  238 HIS
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  191 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 46 optimal weight:    5.9990
   chunk 6 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   chunk 50 optimal weight:    0.6980
   chunk 28 optimal weight:    0.7980
   chunk 76 optimal weight:    6.9990
   chunk 39 optimal weight:    2.9990
   chunk 29 optimal weight:    5.9990
   chunk 65 optimal weight:   10.0000
   chunk 0 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3995 r_free = 0.3995 target = 0.088660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.063412 restraints weight = 27366.736|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 2.34
r_work: 0.3240 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.3275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9605  Z= 0.174
  Angle     :  0.575  13.151  13864  Z= 0.301
  Chirality :  0.035   0.186   1642
  Planarity :  0.004   0.040   1064
  Dihedral  : 22.237 107.746   3431
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 15.44 %
    Favored  : 83.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.63 (0.34), residues: 605
  helix:  2.50 (0.30), residues: 302
  sheet:  0.00 (0.41), residues: 131
  loop : -0.58 (0.47), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  45 
 HIS   0.003   0.001   HIS A 303 
 PHE   0.043   0.002   PHE A 253 
 TYR   0.028   0.001   TYR A 270 
 ARG   0.004   0.000   ARG A 242 

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

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

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 42
  time to evaluate  : 0.925 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7725 (mt-10)
REVERT: A  222 MET cc_start: 0.8228 (ttm) cc_final: 0.7884 (ttm)
REVERT: A  288 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8319 (tp30)
REVERT: A  292 ASP cc_start: 0.8966 (m-30) cc_final: 0.8623 (m-30)
REVERT: B   26 GLN cc_start: 0.8089 (mm110) cc_final: 0.7512 (mm-40)
REVERT: B  156 GLU cc_start: 0.9061 (tm-30) cc_final: 0.8457 (tm-30)
REVERT: B  177 MET cc_start: 0.8571 (mmm) cc_final: 0.8338 (mmm)
  outliers start: 7
  outliers final: 6
  residues processed: 46
  average time/residue: 1.8780
  time to fit residues: 92.4954
Evaluate side-chains
  48 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  238 HIS
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue  191 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 15 optimal weight:    0.8980
   chunk 52 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 65 optimal weight:    9.9990
   chunk 19 optimal weight:    0.6980
   chunk 61 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3998 r_free = 0.3998 target = 0.088819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.063430 restraints weight = 27580.966|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 2.38
r_work: 0.3242 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.3339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9605  Z= 0.178
  Angle     :  0.581  13.087  13864  Z= 0.305
  Chirality :  0.035   0.195   1642
  Planarity :  0.004   0.040   1064
  Dihedral  : 22.216 107.345   3431
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 15.25 %
    Favored  : 83.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.34), residues: 605
  helix:  2.54 (0.30), residues: 301
  sheet: -0.04 (0.41), residues: 131
  loop : -0.60 (0.46), residues: 173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  45 
 HIS   0.003   0.001   HIS A 303 
 PHE   0.049   0.002   PHE A 253 
 TYR   0.019   0.001   TYR A 351 
 ARG   0.003   0.000   ARG A 242 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7771.85 seconds
wall clock time: 137 minutes 27.65 seconds (8247.65 seconds total)