Starting phenix.real_space_refine
on Thu Feb 13 16:29:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dzj_27801/02_2025/8dzj_27801.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dzj_27801/02_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_27801/02_2025/8dzj_27801.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dzj_27801/02_2025/8dzj_27801.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dzj_27801/02_2025/8dzj_27801.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dzj_27801/02_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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.68, per 1000 atoms: 0.63
  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: 2.35
  Conformation dependent library (CDL) restraints added in 585.0 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: 3.72
  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: 3.63

  Time building geometry restraints manager: 2.72 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:             1.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     27.630
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:10.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.810
-------------------------------------------------------------------------------
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  : 1.069 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 89
  average time/residue: 1.3471
  time to fit residues: 127.7448
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  : 0.673 
-------------------------------------------------------------------------------
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 = 35)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.065319 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  : 0.778 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7735 (mt-10)
REVERT: A  222 MET cc_start: 0.8300 (ttm) cc_final: 0.7926 (ttt)
REVERT: A  270 TYR cc_start: 0.4549 (t80) cc_final: 0.4176 (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: 0.8491 (tm-30)
REVERT: B  177 MET cc_start: 0.8433 (mmm) cc_final: 0.8210 (mmm)
  outliers start: 7
  outliers final: 6
  residues processed: 54
  average time/residue: 1.1993
  time to fit residues: 70.4675
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  : 0.707 
-------------------------------------------------------------------------------
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:    1.9990
   overall best weight:    2.1186

-------------------------------------------------------------------------------
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 = 0.3971 r_free = 0.3971 target = 0.088034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.062041 restraints weight = 27086.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 2.36
r_work: 0.3194 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.2001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   9605  Z= 0.279
  Angle     :  0.594   9.441  13864  Z= 0.316
  Chirality :  0.037   0.189   1642
  Planarity :  0.005   0.044   1064
  Dihedral  : 22.533 105.824   3433
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 11.30 %
    Favored  : 87.19 %
  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:  1.51 (0.33), residues: 605
  helix:  2.36 (0.29), residues: 304
  sheet:  0.05 (0.41), residues: 132
  loop : -0.71 (0.45), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  43 
 HIS   0.009   0.002   HIS A 303 
 PHE   0.010   0.002   PHE A 253 
 TYR   0.023   0.002   TYR A 351 
 ARG   0.006   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
  53 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.756 
Fit side-chains
   revert: symmetry clash
REVERT: A  222 MET cc_start: 0.8548 (ttm) cc_final: 0.8089 (ttt)
REVERT: A  288 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8655 (mm-30)
REVERT: A  292 ASP cc_start: 0.8795 (m-30) cc_final: 0.8575 (m-30)
REVERT: B    8 GLU cc_start: 0.7720 (pp20) cc_final: 0.7430 (pp20)
REVERT: B   26 GLN cc_start: 0.8137 (mm110) cc_final: 0.7831 (mm-40)
REVERT: B  137 MET cc_start: 0.7651 (mmp) cc_final: 0.7442 (mmm)
REVERT: B  156 GLU cc_start: 0.9018 (tm-30) cc_final: 0.8736 (tm-30)
REVERT: B  177 MET cc_start: 0.8590 (mmm) cc_final: 0.8329 (mmm)
  outliers start: 8
  outliers final: 5
  residues processed: 50
  average time/residue: 1.2533
  time to fit residues: 67.3735
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  : 0.744 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 48 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 57 optimal weight:   10.0000
   chunk 51 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 45 optimal weight:    3.9990
   chunk 41 optimal weight:    5.9990
   chunk 55 optimal weight:    0.7980
   chunk 58 optimal weight:    3.9990
   overall best weight:    1.7584

-------------------------------------------------------------------------------
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 = 0.088090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.062323 restraints weight = 26773.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 2.30
r_work: 0.3204 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.2276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   9605  Z= 0.238
  Angle     :  0.565   8.286  13864  Z= 0.303
  Chirality :  0.036   0.193   1642
  Planarity :  0.004   0.041   1064
  Dihedral  : 22.455 107.105   3433
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 12.05 %
    Favored  : 86.44 %
  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:  1.49 (0.34), residues: 605
  helix:  2.39 (0.29), residues: 304
  sheet: -0.05 (0.40), residues: 134
  loop : -0.72 (0.46), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  43 
 HIS   0.005   0.001   HIS A 303 
 PHE   0.017   0.002   PHE A 253 
 TYR   0.021   0.001   TYR A 351 
 ARG   0.005   0.000   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
  51 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.760 
Fit side-chains
   revert: symmetry clash
REVERT: A  222 MET cc_start: 0.8474 (ttm) cc_final: 0.8080 (ttm)
REVERT: A  288 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8430 (tp30)
REVERT: A  292 ASP cc_start: 0.8908 (m-30) cc_final: 0.8516 (m-30)
REVERT: B   26 GLN cc_start: 0.8153 (mm110) cc_final: 0.7686 (mm-40)
REVERT: B  156 GLU cc_start: 0.9083 (tm-30) cc_final: 0.8872 (tm-30)
REVERT: B  177 MET cc_start: 0.8618 (mmm) cc_final: 0.8396 (mmm)
  outliers start: 8
  outliers final: 6
  residues processed: 50
  average time/residue: 1.1119
  time to fit residues: 60.3279
Evaluate side-chains
  47 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 VAL
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 46 optimal weight:   10.0000
   chunk 74 optimal weight:    8.9990
   chunk 7 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 60 optimal weight:   10.0000
   chunk 21 optimal weight:   10.0000
   chunk 17 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 28 optimal weight:    3.9990
   chunk 77 optimal weight:    8.9990
   chunk 27 optimal weight:    6.9990
   overall best weight:    2.5788

-------------------------------------------------------------------------------
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 = 0.3934 r_free = 0.3934 target = 0.086039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.060524 restraints weight = 27447.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 2.39
r_work: 0.3162 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.2656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   9605  Z= 0.325
  Angle     :  0.630  10.346  13864  Z= 0.335
  Chirality :  0.039   0.218   1642
  Planarity :  0.005   0.052   1064
  Dihedral  : 22.605 106.347   3433
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 12.62 %
    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:  1.19 (0.33), residues: 605
  helix:  2.15 (0.29), residues: 304
  sheet: -0.13 (0.40), residues: 130
  loop : -0.92 (0.44), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  43 
 HIS   0.006   0.001   HIS A 303 
 PHE   0.019   0.002   PHE A 253 
 TYR   0.019   0.002   TYR A 351 
 ARG   0.004   0.001   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
  52 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 42
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7800 (mt-10)
REVERT: A  222 MET cc_start: 0.8596 (ttm) cc_final: 0.8303 (ttm)
REVERT: A  244 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8707 (pttp)
REVERT: A  288 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8416 (tp30)
REVERT: A  292 ASP cc_start: 0.8901 (m-30) cc_final: 0.8531 (m-30)
REVERT: B   26 GLN cc_start: 0.8223 (mm110) cc_final: 0.7836 (mm-40)
REVERT: B  156 GLU cc_start: 0.9171 (tm-30) cc_final: 0.8524 (tm-30)
REVERT: B  177 MET cc_start: 0.8621 (mmm) cc_final: 0.8419 (mmm)
  outliers start: 10
  outliers final: 8
  residues processed: 49
  average time/residue: 1.4235
  time to fit residues: 74.4783
Evaluate side-chains
  48 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 39
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
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  244 LYS
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    8 GLU
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:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 72 optimal weight:    7.9990
   chunk 27 optimal weight:    0.0270
   chunk 59 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 46 optimal weight:    0.8980
   chunk 10 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 71 optimal weight:    7.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.9440

-------------------------------------------------------------------------------
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 = 0.3990 r_free = 0.3990 target = 0.088797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.063131 restraints weight = 26968.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.3386 rms_B_bonded: 2.33
r_work: 0.3231 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.2814

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= 0.173
  Angle     :  0.557  12.917  13864  Z= 0.294
  Chirality :  0.035   0.191   1642
  Planarity :  0.004   0.041   1064
  Dihedral  : 22.326 108.538   3433
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 11.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 12.62 %
    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:  1.58 (0.34), residues: 605
  helix:  2.44 (0.29), residues: 303
  sheet: -0.02 (0.40), residues: 132
  loop : -0.62 (0.46), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  45 
 HIS   0.003   0.001   HIS A 278 
 PHE   0.026   0.002   PHE A 253 
 TYR   0.021   0.001   TYR A 351 
 ARG   0.004   0.000   ARG B 136 

*********************** 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
  57 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.718 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7777 (mt-10)
REVERT: A  193 ILE cc_start: 0.9038 (pt) cc_final: 0.8834 (pt)
REVERT: A  222 MET cc_start: 0.8313 (ttm) cc_final: 0.8010 (ttm)
REVERT: A  288 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8401 (tp30)
REVERT: A  292 ASP cc_start: 0.8929 (m-30) cc_final: 0.8589 (m-30)
REVERT: B   26 GLN cc_start: 0.8197 (mm110) cc_final: 0.7473 (mm-40)
REVERT: B   30 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7753 (mp0)
REVERT: B   66 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8528 (OUTLIER)
  outliers start: 10
  outliers final: 6
  residues processed: 54
  average time/residue: 1.2526
  time to fit residues: 72.7170
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  : 0.749 
-------------------------------------------------------------------------------
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    8 GLU
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:    0.4980
   chunk 29 optimal weight:    3.9990
   chunk 56 optimal weight:    7.9990
   chunk 45 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0770
   chunk 27 optimal weight:    6.9990
   overall best weight:    2.5144

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

Flipped N/Q/H residues before XYZ refinement:
** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.085998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.060232 restraints weight = 27501.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 2.46
r_work: 0.3158 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.2967

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= 0.323
  Angle     :  0.643  15.193  13864  Z= 0.337
  Chirality :  0.039   0.202   1642
  Planarity :  0.004   0.048   1064
  Dihedral  : 22.517 106.055   3431
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 12.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 13.94 %
    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:  1.31 (0.33), residues: 605
  helix:  2.27 (0.29), residues: 301
  sheet: -0.13 (0.40), residues: 130
  loop : -0.81 (0.44), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  43 
 HIS   0.004   0.001   HIS A 303 
 PHE   0.028   0.002   PHE A 253 
 TYR   0.018   0.002   TYR A 351 
 ARG   0.003   0.000   ARG A 242 

*********************** 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
  53 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.747 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7808 (mt-10)
REVERT: A  222 MET cc_start: 0.8542 (ttm) cc_final: 0.8189 (ttm)
REVERT: A  288 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8367 (tp30)
REVERT: A  292 ASP cc_start: 0.8912 (m-30) cc_final: 0.8547 (m-30)
REVERT: B   26 GLN cc_start: 0.8193 (mm110) cc_final: 0.7680 (mm-40)
REVERT: B  156 GLU cc_start: 0.9002 (tm-30) cc_final: 0.8576 (tm-30)
  outliers start: 9
  outliers final: 7
  residues processed: 50
  average time/residue: 1.2985
  time to fit residues: 69.5344
Evaluate side-chains
  48 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 64 optimal weight:    6.9990
   chunk 56 optimal weight:    0.8980
   chunk 23 optimal weight:    0.6980
   chunk 34 optimal weight:    0.5980
   chunk 39 optimal weight:    6.9990
   chunk 76 optimal weight:    4.9990
   chunk 35 optimal weight:    0.7980
   chunk 43 optimal weight:    4.9990
   chunk 26 optimal weight:    9.9990
   chunk 38 optimal weight:    4.9990
   chunk 45 optimal weight:    4.9990
   overall best weight:    1.5982

-------------------------------------------------------------------------------
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 = 0.3962 r_free = 0.3962 target = 0.087123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.061481 restraints weight = 27674.944|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 2.40
r_work: 0.3188 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.3052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9605  Z= 0.234
  Angle     :  0.604  13.654  13864  Z= 0.316
  Chirality :  0.036   0.196   1642
  Planarity :  0.004   0.039   1064
  Dihedral  : 22.366 107.511   3431
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 11.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 15.82 %
    Favored  : 82.86 %
  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:  1.40 (0.34), residues: 605
  helix:  2.29 (0.29), residues: 302
  sheet: -0.10 (0.40), residues: 132
  loop : -0.66 (0.45), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  45 
 HIS   0.003   0.001   HIS A 278 
 PHE   0.035   0.002   PHE A 253 
 TYR   0.024   0.001   TYR A 270 
 ARG   0.004   0.000   ARG A 242 

*********************** 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
  53 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.665 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7803 (mt-10)
REVERT: A  222 MET cc_start: 0.8421 (ttm) cc_final: 0.8107 (ttm)
REVERT: A  288 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8390 (tp30)
REVERT: A  292 ASP cc_start: 0.8903 (m-30) cc_final: 0.8532 (m-30)
REVERT: B   26 GLN cc_start: 0.8127 (mm110) cc_final: 0.7384 (mm-40)
REVERT: B   30 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7821 (mp0)
REVERT: B   66 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8489 (OUTLIER)
REVERT: B  156 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8657 (tm-30)
  outliers start: 7
  outliers final: 7
  residues processed: 51
  average time/residue: 1.2881
  time to fit residues: 70.5159
Evaluate side-chains
  50 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
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   15 LEU
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:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 69 optimal weight:    8.9990
   chunk 9 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 65 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 23 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   overall best weight:    1.4984

-------------------------------------------------------------------------------
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 = 0.3966 r_free = 0.3966 target = 0.087298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.061867 restraints weight = 27344.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 2.33
r_work: 0.3199 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.3099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9605  Z= 0.229
  Angle     :  0.610  13.394  13864  Z= 0.320
  Chirality :  0.036   0.192   1642
  Planarity :  0.004   0.039   1064
  Dihedral  : 22.331 107.391   3431
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  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:  1.40 (0.34), residues: 605
  helix:  2.33 (0.30), residues: 301
  sheet: -0.12 (0.40), residues: 132
  loop : -0.70 (0.44), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  45 
 HIS   0.003   0.001   HIS A 278 
 PHE   0.044   0.002   PHE A 253 
 TYR   0.019   0.001   TYR A 351 
 ARG   0.003   0.000   ARG B 136 

*********************** 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
  52 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.823 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7778 (mt-10)
REVERT: A  222 MET cc_start: 0.8387 (ttm) cc_final: 0.8075 (ttm)
REVERT: A  288 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8396 (tp30)
REVERT: A  292 ASP cc_start: 0.8906 (m-30) cc_final: 0.8539 (m-30)
REVERT: B   26 GLN cc_start: 0.8125 (mm110) cc_final: 0.7377 (mm-40)
REVERT: B   30 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7831 (mp0)
REVERT: B   66 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8495 (OUTLIER)
REVERT: B  156 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8654 (tm-30)
  outliers start: 9
  outliers final: 7
  residues processed: 49
  average time/residue: 1.3167
  time to fit residues: 69.0923
Evaluate side-chains
  50 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 6 optimal weight:    0.0870
   chunk 4 optimal weight:    0.6980
   chunk 50 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 76 optimal weight:    6.9990
   chunk 39 optimal weight:    8.9990
   chunk 29 optimal weight:    4.9990
   chunk 65 optimal weight:    9.9990
   chunk 0 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   overall best weight:    1.6962

-------------------------------------------------------------------------------
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 = 0.3964 r_free = 0.3964 target = 0.087149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.061503 restraints weight = 27585.575|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 2.39
r_work: 0.3190 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.3149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9605  Z= 0.243
  Angle     :  0.620  13.284  13864  Z= 0.323
  Chirality :  0.037   0.194   1642
  Planarity :  0.004   0.038   1064
  Dihedral  : 22.319 107.228   3431
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 12.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 15.44 %
    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:  1.35 (0.34), residues: 605
  helix:  2.29 (0.29), residues: 302
  sheet: -0.20 (0.41), residues: 131
  loop : -0.69 (0.44), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  45 
 HIS   0.004   0.001   HIS A 278 
 PHE   0.043   0.002   PHE A 253 
 TYR   0.022   0.002   TYR A 270 
 ARG   0.003   0.000   ARG B 136 

********************** 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
  51 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7791 (mt-10)
REVERT: A  222 MET cc_start: 0.8406 (ttm) cc_final: 0.8093 (ttm)
REVERT: A  288 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8400 (tp30)
REVERT: A  292 ASP cc_start: 0.8907 (m-30) cc_final: 0.8540 (m-30)
REVERT: B    8 GLU cc_start: 0.7730 (pp20) cc_final: 0.7206 (pp20)
REVERT: B   26 GLN cc_start: 0.8131 (mm110) cc_final: 0.7393 (mm-40)
REVERT: B   30 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7889 (mp0)
REVERT: B   66 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8484 (OUTLIER)
REVERT: B  156 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8682 (tm-30)
  outliers start: 8
  outliers final: 8
  residues processed: 48
  average time/residue: 1.2983
  time to fit residues: 66.9999
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  : 0.706 
-------------------------------------------------------------------------------
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  168 ILE
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:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 23 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9980
   chunk 65 optimal weight:   10.0000
   chunk 19 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 12 optimal weight:    0.6980
   overall best weight:    1.6984

-------------------------------------------------------------------------------
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 = 0.3961 r_free = 0.3961 target = 0.087193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.061728 restraints weight = 27613.314|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 2.36
r_work: 0.3195 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.3192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9605  Z= 0.243
  Angle     :  0.621  13.122  13864  Z= 0.324
  Chirality :  0.037   0.191   1642
  Planarity :  0.004   0.038   1064
  Dihedral  : 22.313 107.145   3431
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 15.63 %
    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:  1.35 (0.34), residues: 605
  helix:  2.32 (0.30), residues: 301
  sheet: -0.22 (0.41), residues: 131
  loop : -0.73 (0.44), residues: 173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  45 
 HIS   0.004   0.001   HIS A 278 
 PHE   0.049   0.002   PHE A 253 
 TYR   0.019   0.001   TYR A 351 
 ARG   0.003   0.000   ARG B 136 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6997.33 seconds
wall clock time: 124 minutes 5.88 seconds (7445.88 seconds total)