Starting phenix.real_space_refine
on Sat Aug 23 02:29:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dzj_27801/08_2025/8dzj_27801.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dzj_27801/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dzj_27801/08_2025/8dzj_27801.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dzj_27801/08_2025/8dzj_27801.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dzj_27801/08_2025/8dzj_27801.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dzj_27801/08_2025/8dzj_27801.map"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.53, per 1000 atoms: 0.28
  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: 0.99
  Conformation dependent library (CDL) restraints added in 205.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  
  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: 1.61
  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: 1.96

  Time building geometry restraints manager: 1.25 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:             1.630
  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:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     13.380
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:7.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.530
-------------------------------------------------------------------------------
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      :  0.006   0.497   9609  Z= 0.269
  Angle     :  0.706  22.823  13870  Z= 0.365
  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 : 12.59
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.012   0.001   ARG A 291 
 TYR   0.036   0.002   TYR A 233 
 PHE   0.008   0.001   PHE A 336 
 TRP   0.019   0.002   TRP B  43 
 HIS   0.012   0.001   HIS A 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 9605)
  covalent geometry    : angle       0.60380 (13864)
  hydrogen bonds       : bond        0.09213 (  459)
  hydrogen bonds       : angle       5.20261 ( 1170)
  metal coordination   : bond        0.25011 (    4)
  metal coordination   : angle      17.63739 (    6)

*********************** 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  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 89
  average time/residue: 0.6608
  time to fit residues: 62.4249
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  : 0.254 
-------------------------------------------------------------------------------
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 49 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.3980
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    8.9990
   overall best weight:    3.0788

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

Flipped N/Q/H residues before XYZ refinement:
A  56 HIS
A 322 GLN
** B  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 131 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.086438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.060777 restraints weight = 27299.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 2.38
r_work: 0.3162 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.1987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   9609  Z= 0.296
  Angle     :  0.671   8.822  13870  Z= 0.356
  Chirality :  0.041   0.258   1642
  Planarity :  0.005   0.053   1064
  Dihedral  : 22.687 104.879   3433
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 10.17 %
    Favored  : 88.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.05 (0.33), residues: 605
  helix:  1.94 (0.29), residues: 304
  sheet: -0.02 (0.41), residues: 132
  loop : -0.97 (0.42), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 242 
 TYR   0.026   0.002   TYR A 351 
 PHE   0.010   0.002   PHE A 389 
 TRP   0.015   0.002   TRP B  45 
 HIS   0.010   0.002   HIS A 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00624 ( 9605)
  covalent geometry    : angle       0.66263 (13864)
  hydrogen bonds       : bond        0.06045 (  459)
  hydrogen bonds       : angle       4.40236 ( 1170)
  metal coordination   : bond        0.00994 (    4)
  metal coordination   : angle       5.18842 (    6)

*********************** 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
  50 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
REVERT: A  222 MET cc_start: 0.8790 (ttm) cc_final: 0.8398 (ttt)
REVERT: A  288 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8668 (mm-30)
REVERT: A  292 ASP cc_start: 0.8819 (m-30) cc_final: 0.8535 (m-30)
REVERT: B   46 MET cc_start: 0.9110 (mmm) cc_final: 0.8906 (mmm)
REVERT: B  130 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8655 (mm-30)
REVERT: B  155 GLN cc_start: 0.8935 (mm110) cc_final: 0.8714 (mm-40)
REVERT: B  156 GLU cc_start: 0.8835 (tm-30) cc_final: 0.8563 (tm-30)
REVERT: B  177 MET cc_start: 0.8552 (mmm) cc_final: 0.8299 (mmm)
  outliers start: 8
  outliers final: 4
  residues processed: 48
  average time/residue: 0.6031
  time to fit residues: 31.0860
Evaluate side-chains
  40 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
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    8 GLU
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 8 optimal weight:    3.9990
   chunk 75 optimal weight:   10.0000
   chunk 59 optimal weight:    0.0770
   chunk 2 optimal weight:    0.9980
   chunk 69 optimal weight:    8.9990
   chunk 22 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 52 optimal weight:    0.8980
   chunk 71 optimal weight:    7.9990
   chunk 42 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   overall best weight:    1.1140

-------------------------------------------------------------------------------
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 = 0.3994 r_free = 0.3994 target = 0.089104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.063261 restraints weight = 26776.144|
|-----------------------------------------------------------------------------|
r_work (start): 0.3390 rms_B_bonded: 2.32
r_work: 0.3232 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9609  Z= 0.146
  Angle     :  0.551   7.760  13870  Z= 0.293
  Chirality :  0.036   0.197   1642
  Planarity :  0.004   0.042   1064
  Dihedral  : 22.433 108.788   3431
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 10.73 %
    Favored  : 87.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.54 (0.34), residues: 605
  helix:  2.46 (0.29), residues: 304
  sheet: -0.05 (0.40), residues: 134
  loop : -0.75 (0.45), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 242 
 TYR   0.022   0.001   TYR A 351 
 PHE   0.018   0.001   PHE A 253 
 TRP   0.008   0.001   TRP B  45 
 HIS   0.004   0.001   HIS A 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 9605)
  covalent geometry    : angle       0.54431 (13864)
  hydrogen bonds       : bond        0.04788 (  459)
  hydrogen bonds       : angle       4.11604 ( 1170)
  metal coordination   : bond        0.00664 (    4)
  metal coordination   : angle       4.03122 (    6)

*********************** 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
  55 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
REVERT: A  222 MET cc_start: 0.8429 (ttm) cc_final: 0.8032 (ttt)
REVERT: A  288 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8592 (mm-30)
REVERT: A  324 GLU cc_start: 0.7914 (pp20) cc_final: 0.7582 (pp20)
REVERT: B   26 GLN cc_start: 0.8092 (mm-40) cc_final: 0.7633 (mm-40)
REVERT: B   46 MET cc_start: 0.9105 (mmm) cc_final: 0.8885 (mmm)
REVERT: B  130 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8600 (mm-30)
REVERT: B  156 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8506 (tm-30)
REVERT: B  177 MET cc_start: 0.8643 (mmm) cc_final: 0.8407 (mmm)
  outliers start: 10
  outliers final: 6
  residues processed: 53
  average time/residue: 0.5650
  time to fit residues: 32.2500
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  : 0.260 
-------------------------------------------------------------------------------
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 57 optimal weight:    6.9990
   chunk 65 optimal weight:    9.9990
   chunk 3 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 26 optimal weight:    8.9990
   chunk 11 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 47 optimal weight:    4.9990
   chunk 37 optimal weight:   20.0000
   overall best weight:    2.3990

-------------------------------------------------------------------------------
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 = 0.3943 r_free = 0.3943 target = 0.086455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.060753 restraints weight = 27539.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 2.35
r_work: 0.3169 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
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      :  0.005   0.034   9609  Z= 0.239
  Angle     :  0.620   8.779  13870  Z= 0.326
  Chirality :  0.039   0.205   1642
  Planarity :  0.005   0.048   1064
  Dihedral  : 22.589 105.852   3431
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 12.05 %
    Favored  : 85.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.32 (0.33), residues: 605
  helix:  2.28 (0.29), residues: 304
  sheet: -0.13 (0.41), residues: 130
  loop : -0.86 (0.43), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 291 
 TYR   0.020   0.002   TYR A 351 
 PHE   0.017   0.002   PHE A 253 
 TRP   0.013   0.002   TRP B  43 
 HIS   0.006   0.001   HIS A 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00504 ( 9605)
  covalent geometry    : angle       0.61365 (13864)
  hydrogen bonds       : bond        0.05544 (  459)
  hydrogen bonds       : angle       4.21255 ( 1170)
  metal coordination   : bond        0.00944 (    4)
  metal coordination   : angle       4.34556 (    6)

*********************** 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: 11
    poor density    : 40
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
REVERT: A  222 MET cc_start: 0.8600 (ttm) cc_final: 0.8221 (ttm)
REVERT: B   26 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7716 (mm-40)
REVERT: B   46 MET cc_start: 0.9102 (mmm) cc_final: 0.8888 (mmm)
REVERT: B  130 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8649 (mm-30)
REVERT: B  156 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8588 (tm-30)
REVERT: B  177 MET cc_start: 0.8591 (mmm) cc_final: 0.8359 (mmm)
  outliers start: 11
  outliers final: 7
  residues processed: 49
  average time/residue: 0.5813
  time to fit residues: 30.6703
Evaluate side-chains
  43 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 36
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  337 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 37 optimal weight:   20.0000
   chunk 65 optimal weight:    9.9990
   chunk 63 optimal weight:    5.9990
   chunk 46 optimal weight:    8.9990
   chunk 69 optimal weight:    6.9990
   chunk 72 optimal weight:    7.9990
   chunk 27 optimal weight:    0.1980
   chunk 43 optimal weight:    5.9990
   chunk 11 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    3.0388

-------------------------------------------------------------------------------
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 = 0.3918 r_free = 0.3918 target = 0.085088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.059636 restraints weight = 27530.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 2.37
r_work: 0.3142 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.2876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050   9609  Z= 0.284
  Angle     :  0.663  10.685  13870  Z= 0.346
  Chirality :  0.041   0.251   1642
  Planarity :  0.005   0.052   1064
  Dihedral  : 22.657 106.395   3431
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 12.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 12.81 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.07 (0.33), residues: 605
  helix:  2.07 (0.29), residues: 304
  sheet: -0.25 (0.40), residues: 129
  loop : -0.97 (0.43), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 291 
 TYR   0.019   0.002   TYR A 351 
 PHE   0.017   0.002   PHE A 253 
 TRP   0.016   0.002   TRP B  43 
 HIS   0.005   0.002   HIS A 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00600 ( 9605)
  covalent geometry    : angle       0.65524 (13864)
  hydrogen bonds       : bond        0.05887 (  459)
  hydrogen bonds       : angle       4.29886 ( 1170)
  metal coordination   : bond        0.01122 (    4)
  metal coordination   : angle       4.83540 (    6)

*********************** 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: 12
    poor density    : 40
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
REVERT: A  222 MET cc_start: 0.8667 (ttm) cc_final: 0.8311 (ttm)
REVERT: B   46 MET cc_start: 0.9086 (mmm) cc_final: 0.8837 (mmm)
REVERT: B  130 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8664 (mm-30)
REVERT: B  156 GLU cc_start: 0.8992 (tm-30) cc_final: 0.8606 (tm-30)
REVERT: B  177 MET cc_start: 0.8582 (mmm) cc_final: 0.8347 (mmm)
  outliers start: 12
  outliers final: 9
  residues processed: 49
  average time/residue: 0.6368
  time to fit residues: 33.4154
Evaluate side-chains
  46 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 37
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
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  337 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
Chi-restraints excluded: chain B residue  191 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 55 optimal weight:    6.9990
   chunk 40 optimal weight:    5.9990
   chunk 59 optimal weight:    0.8980
   chunk 63 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 66 optimal weight:    9.9990
   chunk 67 optimal weight:    9.9990
   chunk 8 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    2.3386

-------------------------------------------------------------------------------
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 = 0.3929 r_free = 0.3929 target = 0.085624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.060167 restraints weight = 27430.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 2.37
r_work: 0.3158 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.2995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   9609  Z= 0.231
  Angle     :  0.623  11.352  13870  Z= 0.328
  Chirality :  0.039   0.212   1642
  Planarity :  0.004   0.046   1064
  Dihedral  : 22.585 108.103   3431
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 12.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 14.12 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.18 (0.34), residues: 605
  helix:  2.14 (0.30), residues: 304
  sheet: -0.20 (0.41), residues: 129
  loop : -0.87 (0.44), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 291 
 TYR   0.020   0.002   TYR A 351 
 PHE   0.024   0.002   PHE A 253 
 TRP   0.012   0.002   TRP B  45 
 HIS   0.004   0.001   HIS A 278 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 ( 9605)
  covalent geometry    : angle       0.61575 (13864)
  hydrogen bonds       : bond        0.05492 (  459)
  hydrogen bonds       : angle       4.25025 ( 1170)
  metal coordination   : bond        0.00952 (    4)
  metal coordination   : angle       4.54361 (    6)

*********************** 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
  53 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
REVERT: A  222 MET cc_start: 0.8593 (ttm) cc_final: 0.8290 (ttm)
REVERT: B   26 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7730 (mm-40)
REVERT: B   46 MET cc_start: 0.9104 (mmm) cc_final: 0.8828 (mmm)
REVERT: B  130 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8639 (mm-30)
REVERT: B  156 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8634 (tm-30)
REVERT: B  177 MET cc_start: 0.8600 (mmm) cc_final: 0.8355 (mmm)
  outliers start: 11
  outliers final: 10
  residues processed: 50
  average time/residue: 0.5152
  time to fit residues: 27.8595
Evaluate side-chains
  48 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 38
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
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  324 GLU
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
Chi-restraints excluded: chain B residue  191 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 35 optimal weight:    0.4980
   chunk 21 optimal weight:    0.9980
   chunk 71 optimal weight:    8.9990
   chunk 32 optimal weight:    0.9980
   chunk 38 optimal weight:    6.9990
   chunk 4 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 67 optimal weight:   10.0000
   overall best weight:    1.2982

-------------------------------------------------------------------------------
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 = 0.3959 r_free = 0.3959 target = 0.086980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.061690 restraints weight = 27329.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 2.31
r_work: 0.3194 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.3061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9609  Z= 0.160
  Angle     :  0.586  13.733  13870  Z= 0.309
  Chirality :  0.036   0.200   1642
  Planarity :  0.004   0.040   1064
  Dihedral  : 22.421 108.662   3431
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 14.88 %
    Favored  : 83.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.42 (0.34), residues: 605
  helix:  2.35 (0.30), residues: 302
  sheet: -0.15 (0.41), residues: 131
  loop : -0.70 (0.45), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 242 
 TYR   0.023   0.001   TYR A 270 
 PHE   0.029   0.002   PHE A 253 
 TRP   0.010   0.001   TRP B  45 
 HIS   0.003   0.001   HIS A 278 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 9605)
  covalent geometry    : angle       0.58091 (13864)
  hydrogen bonds       : bond        0.05084 (  459)
  hydrogen bonds       : angle       4.16321 ( 1170)
  metal coordination   : bond        0.00671 (    4)
  metal coordination   : angle       3.85190 (    6)

*********************** 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
  50 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 41
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
REVERT: A  222 MET cc_start: 0.8481 (ttm) cc_final: 0.8188 (ttm)
REVERT: B   26 GLN cc_start: 0.8248 (mm-40) cc_final: 0.7536 (mm-40)
REVERT: B   30 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7848 (mp0)
REVERT: B   66 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8499 (OUTLIER)
REVERT: B  130 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8630 (mm-30)
REVERT: B  156 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8646 (tm-30)
REVERT: B  177 MET cc_start: 0.8598 (mmm) cc_final: 0.8348 (mmm)
  outliers start: 9
  outliers final: 9
  residues processed: 47
  average time/residue: 0.4075
  time to fit residues: 20.7156
Evaluate side-chains
  50 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 41
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
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  337 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
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 30 optimal weight:    0.8980
   chunk 76 optimal weight:    5.9990
   chunk 75 optimal weight:   10.0000
   chunk 77 optimal weight:    8.9990
   chunk 45 optimal weight:    4.9990
   chunk 46 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 63 optimal weight:    4.9990
   chunk 66 optimal weight:    9.9990
   overall best weight:    2.1384

-------------------------------------------------------------------------------
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 = 0.3940 r_free = 0.3940 target = 0.086065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.060715 restraints weight = 27512.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 2.36
r_work: 0.3173 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.3176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   9609  Z= 0.218
  Angle     :  0.630  14.029  13870  Z= 0.329
  Chirality :  0.038   0.197   1642
  Planarity :  0.004   0.046   1064
  Dihedral  : 22.458 107.268   3431
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 11.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 14.88 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.32 (0.34), residues: 605
  helix:  2.29 (0.29), residues: 302
  sheet: -0.22 (0.41), residues: 131
  loop : -0.74 (0.45), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 242 
 TYR   0.020   0.001   TYR A 351 
 PHE   0.034   0.003   PHE A 253 
 TRP   0.009   0.001   TRP B  43 
 HIS   0.004   0.001   HIS A 278 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 ( 9605)
  covalent geometry    : angle       0.62422 (13864)
  hydrogen bonds       : bond        0.05427 (  459)
  hydrogen bonds       : angle       4.21330 ( 1170)
  metal coordination   : bond        0.00875 (    4)
  metal coordination   : angle       4.09656 (    6)

*********************** 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
  54 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 42
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 MET cc_start: 0.8504 (ttm) cc_final: 0.8213 (ttm)
REVERT: B   26 GLN cc_start: 0.8254 (mm-40) cc_final: 0.7544 (mm-40)
REVERT: B   30 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7930 (mp0)
REVERT: B   46 MET cc_start: 0.9087 (mmm) cc_final: 0.8876 (mmm)
REVERT: B   66 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8431 (OUTLIER)
REVERT: B  130 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8659 (mm-30)
REVERT: B  156 GLU cc_start: 0.9023 (tm-30) cc_final: 0.8504 (tm-30)
REVERT: B  177 MET cc_start: 0.8602 (mmm) cc_final: 0.8358 (mmm)
  outliers start: 12
  outliers final: 10
  residues processed: 51
  average time/residue: 0.4988
  time to fit residues: 27.4281
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  : 0.147 
-------------------------------------------------------------------------------
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  324 GLU
Chi-restraints excluded: chain A residue  337 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
Chi-restraints excluded: chain B residue  191 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 46 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9990
   chunk 69 optimal weight:    9.9990
   chunk 35 optimal weight:    0.0980
   chunk 45 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A 346 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 = 0.3995 r_free = 0.3995 target = 0.088675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.063455 restraints weight = 27271.623|
|-----------------------------------------------------------------------------|
r_work (start): 0.3400 rms_B_bonded: 2.33
r_work: 0.3242 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.3311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9609  Z= 0.134
  Angle     :  0.582  12.668  13870  Z= 0.304
  Chirality :  0.035   0.191   1642
  Planarity :  0.004   0.041   1064
  Dihedral  : 22.280 108.688   3431
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 15.82 %
    Favored  : 82.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.52 (0.34), residues: 605
  helix:  2.36 (0.30), residues: 303
  sheet: -0.09 (0.41), residues: 131
  loop : -0.53 (0.46), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 242 
 TYR   0.023   0.001   TYR A 270 
 PHE   0.040   0.003   PHE A 253 
 TRP   0.007   0.001   TRP B  45 
 HIS   0.006   0.001   HIS B  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 9605)
  covalent geometry    : angle       0.57805 (13864)
  hydrogen bonds       : bond        0.04889 (  459)
  hydrogen bonds       : angle       4.08554 ( 1170)
  metal coordination   : bond        0.00466 (    4)
  metal coordination   : angle       3.15401 (    6)

*********************** 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
  50 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 MET cc_start: 0.8374 (ttm) cc_final: 0.8063 (ttm)
REVERT: A  270 TYR cc_start: 0.5166 (t80) cc_final: 0.4931 (t80)
REVERT: B   26 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7541 (mm-40)
REVERT: B  130 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8585 (mm-30)
REVERT: B  177 MET cc_start: 0.8586 (mmm) cc_final: 0.8339 (mmm)
  outliers start: 8
  outliers final: 9
  residues processed: 48
  average time/residue: 0.4779
  time to fit residues: 24.7775
Evaluate side-chains
  49 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 40
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
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  324 GLU
Chi-restraints excluded: chain A residue  337 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 69 optimal weight:   10.0000
   chunk 72 optimal weight:    8.9990
   chunk 3 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 346 GLN
B 155 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.088500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.063228 restraints weight = 27372.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 2.34
r_work: 0.3235 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.3405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9609  Z= 0.143
  Angle     :  0.593  13.087  13870  Z= 0.310
  Chirality :  0.035   0.177   1642
  Planarity :  0.004   0.040   1064
  Dihedral  : 22.252 107.261   3431
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 15.63 %
    Favored  : 82.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.58 (0.34), residues: 605
  helix:  2.44 (0.30), residues: 302
  sheet: -0.01 (0.42), residues: 131
  loop : -0.58 (0.46), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 242 
 TYR   0.022   0.001   TYR A 270 
 PHE   0.049   0.003   PHE A 253 
 TRP   0.006   0.001   TRP B  45 
 HIS   0.005   0.001   HIS B  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 9605)
  covalent geometry    : angle       0.58975 (13864)
  hydrogen bonds       : bond        0.04910 (  459)
  hydrogen bonds       : angle       4.04989 ( 1170)
  metal coordination   : bond        0.00489 (    4)
  metal coordination   : angle       2.95025 (    6)

********************** 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
  52 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 41
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 MET cc_start: 0.8283 (ttm) cc_final: 0.7993 (ttm)
REVERT: A  270 TYR cc_start: 0.5116 (t80) cc_final: 0.4833 (t80)
REVERT: B    8 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7085 (pp20)
REVERT: B   26 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7549 (mm-40)
REVERT: B  130 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8667 (mm-30)
REVERT: B  156 GLU cc_start: 0.8952 (tm-30) cc_final: 0.8391 (tm-30)
REVERT: B  177 MET cc_start: 0.8590 (mmm) cc_final: 0.8334 (mmm)
  outliers start: 11
  outliers final: 8
  residues processed: 47
  average time/residue: 0.4788
  time to fit residues: 24.3405
Evaluate side-chains
  49 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 40
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
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  324 GLU
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  191 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 54 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 69 optimal weight:    9.9990
   chunk 75 optimal weight:   10.0000
   chunk 28 optimal weight:    0.5980
   chunk 58 optimal weight:    9.9990
   chunk 15 optimal weight:    0.9990
   chunk 26 optimal weight:    4.9990
   chunk 62 optimal weight:    5.9990
   overall best weight:    0.8784

-------------------------------------------------------------------------------
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 = 0.088795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.063622 restraints weight = 27129.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 2.33
r_work: 0.3244 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.3443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9609  Z= 0.139
  Angle     :  0.591  13.111  13870  Z= 0.310
  Chirality :  0.035   0.176   1642
  Planarity :  0.004   0.040   1064
  Dihedral  : 22.236 107.039   3431
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 16.38 %
    Favored  : 81.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.56 (0.34), residues: 605
  helix:  2.43 (0.30), residues: 302
  sheet: -0.02 (0.42), residues: 131
  loop : -0.62 (0.46), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 242 
 TYR   0.022   0.001   TYR A 270 
 PHE   0.055   0.003   PHE A 253 
 TRP   0.006   0.001   TRP B  45 
 HIS   0.005   0.001   HIS B  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 9605)
  covalent geometry    : angle       0.58837 (13864)
  hydrogen bonds       : bond        0.04873 (  459)
  hydrogen bonds       : angle       4.04961 ( 1170)
  metal coordination   : bond        0.00448 (    4)
  metal coordination   : angle       2.88295 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3307.10 seconds
wall clock time: 57 minutes 13.56 seconds (3433.56 seconds total)