Starting phenix.real_space_refine
on Thu Jul  2 15:48:17 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8dzj_27801/07_2026/8dzj_27801.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dzj_27801/07_2026/8dzj_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 {
    restraint_files = "/net/cci-nas-00/data/ceres_data/8dzj_27801/07_2026/8dzj_27801.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8dzj_27801/07_2026/8dzj_27801.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dzj_27801/07_2026/8dzj_27801.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dzj_27801/07_2026/8dzj_27801.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dzj_27801/07_2026/8dzj_27801.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dzj_27801/07_2026/8dzj_27801.cif"
  }
  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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 1.37, per 1000 atoms: 0.15
  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: 0.80
  Conformation dependent library (CDL) restraints added in 134.4 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: 1.02
  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: 1.47

  Time building geometry restraints manager: 0.96 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=" C1'  DT C  20 "
       pdb=" N1   DT C  20 "
    ideal  model  delta    sigma   weight residual
    1.468  1.517 -0.049 1.40e-02 5.10e+03 1.24e+01
  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=" C3'  DA C  32 "
       pdb=" C2'  DA C  32 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 9.32e+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
  ... (remaining 9600 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.41: 13219
        1.41 -     2.81: 561
        2.81 -     4.22: 69
        4.22 -     5.63: 13
        5.63 -     7.04: 2
  Bond angle restraints: 13864
  Sorted by residual:
  angle pdb=" O4'  DC C  35 "
        pdb=" C4'  DC C  35 "
        pdb=" C3'  DC C  35 "
      ideal   model   delta    sigma   weight residual
     106.00  103.19    2.81 6.00e-01 2.78e+00 2.19e+01
  angle pdb=" N3   DT C  20 "
        pdb=" C4   DT C  20 "
        pdb=" O4   DT C  20 "
      ideal   model   delta    sigma   weight residual
     119.90  122.60   -2.70 6.00e-01 2.78e+00 2.02e+01
  angle pdb=" N3   DT C  22 "
        pdb=" C4   DT C  22 "
        pdb=" O4   DT C  22 "
      ideal   model   delta    sigma   weight residual
     119.90  122.54   -2.64 6.00e-01 2.78e+00 1.94e+01
  angle pdb=" N3   DT C  16 "
        pdb=" C4   DT C  16 "
        pdb=" O4   DT C  16 "
      ideal   model   delta    sigma   weight residual
     119.90  122.51   -2.61 6.00e-01 2.78e+00 1.90e+01
  angle pdb=" N3   DT D  10 "
        pdb=" C4   DT D  10 "
        pdb=" O4   DT D  10 "
      ideal   model   delta    sigma   weight residual
     119.90  122.50   -2.60 6.00e-01 2.78e+00 1.88e+01
  ... (remaining 13859 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.54: 4715
       21.54 -    43.09: 434
       43.09 -    64.63: 162
       64.63 -    86.17: 8
       86.17 -   107.71: 6
  Dihedral angle restraints: 5325
    sinusoidal: 3530
      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 5322 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 1436
       0.060 -    0.119: 178
       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:             1.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.180
  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:7.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7097
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= 0.335
  Angle     :  0.736  22.823  13870  Z= 0.442
  Chirality :  0.041   0.298   1642
  Planarity :  0.004   0.038   1064
  Dihedral  : 16.635 107.713   4177
  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 are 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/Z
  covalent geometry    : bond        0.00399 /  0.29 ( 9605)
  covalent geometry    : angle       0.63794 /  0.44 (13864)
  hydrogen bonds       : bond        0.09213 /  5.64 (  459)
  hydrogen bonds       : angle       5.20261 /  3.68 ( 1170)
  metal coordination   : bond        0.25011 / 16.65 (    4)
  metal coordination   : angle      17.63739 / 10.67 (    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  : 0.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 89
  average time/residue: 0.4916
  time to fit residues: 46.6858
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  : 0.163 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:   10.0000
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    8.9990
   overall best weight:    3.2788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 322 GLN
** B  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.088006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.061941 restraints weight = 26903.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 2.41
r_work: 0.3185 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.1440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   9609  Z= 0.304
  Angle     :  0.684  11.850  13870  Z= 0.363
  Chirality :  0.042   0.236   1642
  Planarity :  0.006   0.054   1064
  Dihedral  : 17.064 106.615   2925
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  :  8.47 %
    Favored  : 89.64 %
  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 are not related in a simple way.
  whole:  0.96 (0.33), residues: 605
  helix:  1.86 (0.29), residues: 303
  sheet: -0.10 (0.40), residues: 134
  loop : -0.94 (0.43), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 261 
 TYR   0.026   0.002   TYR A 351 
 PHE   0.009   0.002   PHE A 236 
 TRP   0.015   0.002   TRP B  45 
 HIS   0.009   0.002   HIS A 303 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00628 /  0.30 ( 9605)
  covalent geometry    : angle       0.67425 /  0.36 (13864)
  hydrogen bonds       : bond        0.05934 /  3.59 (  459)
  hydrogen bonds       : angle       4.49749 /  3.27 ( 1170)
  metal coordination   : bond        0.02676 /  1.85 (    4)
  metal coordination   : angle       5.54116 /  3.73 (    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
  52 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 42
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7824 (mt-10)
REVERT: A  222 MET cc_start: 0.8558 (ttm) cc_final: 0.8158 (ttt)
REVERT: B  156 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8374 (tm-30)
REVERT: B  177 MET cc_start: 0.8528 (mmm) cc_final: 0.8263 (mmm)
  outliers start: 10
  outliers final: 7
  residues processed: 50
  average time/residue: 0.5625
  time to fit residues: 30.1872
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  : 0.247 
-------------------------------------------------------------------------------
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   15 LEU
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  204 ASN
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:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 69 optimal weight:    8.9990
   chunk 22 optimal weight:    4.9990
   chunk 18 optimal weight:    5.9990
   chunk 52 optimal weight:    4.9990
   chunk 71 optimal weight:    7.9990
   chunk 42 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    2.7788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  56 HIS
A 366 GLN
B  26 GLN
** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.087561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.061499 restraints weight = 27038.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 2.37
r_work: 0.3173 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.1724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   9609  Z= 0.254
  Angle     :  0.632  10.146  13870  Z= 0.335
  Chirality :  0.040   0.219   1642
  Planarity :  0.005   0.046   1064
  Dihedral  : 17.017 106.085   2923
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 11.86 %
    Favored  : 86.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.03 (0.33), residues: 605
  helix:  2.00 (0.29), residues: 303
  sheet: -0.18 (0.40), residues: 134
  loop : -0.96 (0.45), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 242 
 TYR   0.023   0.002   TYR A 351 
 PHE   0.013   0.002   PHE A 253 
 TRP   0.015   0.002   TRP B  43 
 HIS   0.006   0.002   HIS A 303 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00524 /  0.25 ( 9605)
  covalent geometry    : angle       0.62268 /  0.33 (13864)
  hydrogen bonds       : bond        0.05697 /  3.43 (  459)
  hydrogen bonds       : angle       4.39934 /  3.22 ( 1170)
  metal coordination   : bond        0.01242 /  0.74 (    4)
  metal coordination   : angle       5.17359 /  3.36 (    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
  48 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.165 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7845 (mt-10)
REVERT: A  222 MET cc_start: 0.8601 (ttm) cc_final: 0.8174 (ttt)
REVERT: B  156 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8553 (tm-30)
REVERT: B  177 MET cc_start: 0.8572 (mmm) cc_final: 0.8314 (mmm)
  outliers start: 7
  outliers final: 5
  residues processed: 46
  average time/residue: 0.4197
  time to fit residues: 20.9011
Evaluate side-chains
  44 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
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   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:    3.9990
   chunk 57 optimal weight:    4.9990
   chunk 65 optimal weight:    9.9990
   chunk 3 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 26 optimal weight:    8.9990
   chunk 11 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 18 optimal weight:    0.8980
   chunk 47 optimal weight:    3.9990
   chunk 37 optimal weight:   20.0000
   overall best weight:    1.9186

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.087912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.062090 restraints weight = 27269.114|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 2.32
r_work: 0.3191 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.1881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9609  Z= 0.197
  Angle     :  0.593   8.839  13870  Z= 0.317
  Chirality :  0.038   0.205   1642
  Planarity :  0.004   0.044   1064
  Dihedral  : 16.990 106.777   2923
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 12.43 %
    Favored  : 85.69 %
  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 are not related in a simple way.
  whole:  1.22 (0.33), residues: 605
  helix:  2.19 (0.29), residues: 303
  sheet: -0.14 (0.40), residues: 134
  loop : -0.91 (0.45), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 242 
 TYR   0.022   0.001   TYR A 351 
 PHE   0.019   0.002   PHE A 253 
 TRP   0.012   0.002   TRP B  43 
 HIS   0.004   0.001   HIS A 303 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00401 /  0.20 ( 9605)
  covalent geometry    : angle       0.58632 /  0.32 (13864)
  hydrogen bonds       : bond        0.05325 /  3.24 (  459)
  hydrogen bonds       : angle       4.28302 /  3.13 ( 1170)
  metal coordination   : bond        0.00901 /  0.52 (    4)
  metal coordination   : angle       4.37289 /  2.71 (    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
  54 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 44
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7829 (mt-10)
REVERT: A  222 MET cc_start: 0.8576 (ttm) cc_final: 0.8207 (ttm)
REVERT: A  244 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8716 (pttp)
REVERT: A  288 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8674 (mm-30)
REVERT: A  292 ASP cc_start: 0.8791 (m-30) cc_final: 0.8509 (m-30)
REVERT: B  137 MET cc_start: 0.7207 (mpp) cc_final: 0.6785 (mpm)
REVERT: B  156 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8478 (tm-30)
REVERT: B  177 MET cc_start: 0.8673 (mmm) cc_final: 0.8443 (mmm)
  outliers start: 10
  outliers final: 7
  residues processed: 52
  average time/residue: 0.4359
  time to fit residues: 24.3103
Evaluate side-chains
  48 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 VAL
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 37 optimal weight:    0.4980
   chunk 65 optimal weight:    9.9990
   chunk 63 optimal weight:    5.9990
   chunk 46 optimal weight:    6.9990
   chunk 69 optimal weight:    6.9990
   chunk 72 optimal weight:    7.9990
   chunk 27 optimal weight:    0.9980
   chunk 43 optimal weight:    5.9990
   chunk 11 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    2.6986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 131 ASN ** 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 = 0.3948 r_free = 0.3948 target = 0.086832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.060968 restraints weight = 27147.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.3324 rms_B_bonded: 2.36
r_work: 0.3167 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.2099

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= 0.252
  Angle     :  0.630   9.820  13870  Z= 0.335
  Chirality :  0.040   0.220   1642
  Planarity :  0.005   0.047   1064
  Dihedral  : 17.019 106.816   2923
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 13.37 %
    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 are not related in a simple way.
  whole:  1.16 (0.33), residues: 605
  helix:  2.16 (0.29), residues: 303
  sheet: -0.23 (0.40), residues: 134
  loop : -0.93 (0.45), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 242 
 TYR   0.021   0.002   TYR A 351 
 PHE   0.021   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/Z
  covalent geometry    : bond        0.00518 /  0.25 ( 9605)
  covalent geometry    : angle       0.62348 /  0.33 (13864)
  hydrogen bonds       : bond        0.05631 /  3.45 (  459)
  hydrogen bonds       : angle       4.28245 /  3.14 ( 1170)
  metal coordination   : bond        0.01016 /  0.58 (    4)
  metal coordination   : angle       4.22736 /  2.63 (    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: 9
    poor density    : 43
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7813 (mt-10)
REVERT: A  157 MET cc_start: 0.8722 (mmm) cc_final: 0.8494 (tpp)
REVERT: A  222 MET cc_start: 0.8596 (ttm) cc_final: 0.8213 (ttm)
REVERT: A  244 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8729 (pttp)
REVERT: A  288 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8119 (mm-30)
REVERT: A  292 ASP cc_start: 0.8777 (m-30) cc_final: 0.8282 (m-30)
REVERT: B   26 GLN cc_start: 0.8040 (mm110) cc_final: 0.7785 (mm-40)
REVERT: B  156 GLU cc_start: 0.8981 (tm-30) cc_final: 0.8533 (tm-30)
REVERT: B  177 MET cc_start: 0.8677 (mmm) cc_final: 0.8449 (mmm)
  outliers start: 9
  outliers final: 7
  residues processed: 50
  average time/residue: 0.4517
  time to fit residues: 24.3421
Evaluate side-chains
  49 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 41
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 VAL
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 55 optimal weight:    0.7980
   chunk 40 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9980
   chunk 63 optimal weight:    5.9990
   chunk 22 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   chunk 6 optimal weight:    0.0040
   chunk 66 optimal weight:   10.0000
   chunk 67 optimal weight:   10.0000
   chunk 8 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.6994

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 131 ASN ** 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 = 0.3991 r_free = 0.3991 target = 0.088924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.063054 restraints weight = 26744.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.3382 rms_B_bonded: 2.32
r_work: 0.3225 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.2145

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= 0.132
  Angle     :  0.554   7.845  13870  Z= 0.298
  Chirality :  0.036   0.202   1642
  Planarity :  0.004   0.043   1064
  Dihedral  : 16.913 107.610   2923
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 13.75 %
    Favored  : 84.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.56 (0.34), residues: 605
  helix:  2.49 (0.29), residues: 303
  sheet: -0.11 (0.40), residues: 134
  loop : -0.68 (0.46), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 242 
 TYR   0.018   0.001   TYR A 351 
 PHE   0.025   0.002   PHE A 253 
 TRP   0.007   0.001   TRP B  45 
 HIS   0.002   0.001   HIS B  72 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00257 /  0.13 ( 9605)
  covalent geometry    : angle       0.54913 /  0.30 (13864)
  hydrogen bonds       : bond        0.04959 /  3.04 (  459)
  hydrogen bonds       : angle       4.17137 /  3.05 ( 1170)
  metal coordination   : bond        0.00530 /  0.30 (    4)
  metal coordination   : angle       3.53057 /  2.12 (    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
  56 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7784 (mt-10)
REVERT: A  193 ILE cc_start: 0.8994 (pt) cc_final: 0.8790 (pt)
REVERT: A  222 MET cc_start: 0.8343 (ttm) cc_final: 0.7995 (ttm)
REVERT: A  244 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8690 (pttp)
REVERT: A  288 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8019 (mm-30)
REVERT: A  292 ASP cc_start: 0.8745 (m-30) cc_final: 0.8200 (m-30)
REVERT: B   26 GLN cc_start: 0.8075 (mm110) cc_final: 0.7659 (mm-40)
REVERT: B  137 MET cc_start: 0.5929 (mpp) cc_final: 0.5725 (mpm)
REVERT: B  156 GLU cc_start: 0.8992 (tm-30) cc_final: 0.8499 (tm-30)
REVERT: B  177 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8450 (mmm)
  outliers start: 10
  outliers final: 7
  residues processed: 51
  average time/residue: 0.5919
  time to fit residues: 32.4595
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  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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
Chi-restraints excluded: chain B residue  177 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 21 optimal weight:   10.0000
   chunk 71 optimal weight:    8.9990
   chunk 32 optimal weight:    5.9990
   chunk 38 optimal weight:    8.9990
   chunk 4 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   chunk 7 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 67 optimal weight:   10.0000
   overall best weight:    2.9386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 131 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.086609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.060710 restraints weight = 27183.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 2.44
r_work: 0.3164 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.2325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   9609  Z= 0.267
  Angle     :  0.621  10.006  13870  Z= 0.333
  Chirality :  0.040   0.210   1642
  Planarity :  0.005   0.054   1064
  Dihedral  : 16.973 107.274   2923
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 12.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 14.31 %
    Favored  : 83.99 %
  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 are not related in a simple way.
  whole:  1.28 (0.33), residues: 605
  helix:  2.28 (0.29), residues: 303
  sheet: -0.28 (0.40), residues: 133
  loop : -0.83 (0.45), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 101 
 TYR   0.020   0.002   TYR A 351 
 PHE   0.026   0.002   PHE A 253 
 TRP   0.017   0.002   TRP B  43 
 HIS   0.005   0.001   HIS A 278 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00549 /  0.27 ( 9605)
  covalent geometry    : angle       0.61623 /  0.33 (13864)
  hydrogen bonds       : bond        0.05625 /  3.46 (  459)
  hydrogen bonds       : angle       4.24080 /  3.11 ( 1170)
  metal coordination   : bond        0.00954 /  0.55 (    4)
  metal coordination   : angle       3.74451 /  2.31 (    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
  51 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 42
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7844 (mt-10)
REVERT: A  222 MET cc_start: 0.8574 (ttm) cc_final: 0.8207 (ttm)
REVERT: A  244 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8726 (pttp)
REVERT: A  288 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8067 (mm-30)
REVERT: A  292 ASP cc_start: 0.8757 (m-30) cc_final: 0.8240 (m-30)
REVERT: B   26 GLN cc_start: 0.8114 (mm110) cc_final: 0.7685 (mm-40)
REVERT: B  137 MET cc_start: 0.6072 (mpp) cc_final: 0.5798 (mpm)
REVERT: B  177 MET cc_start: 0.8609 (mmm) cc_final: 0.8357 (mmm)
  outliers start: 9
  outliers final: 8
  residues processed: 48
  average time/residue: 0.5603
  time to fit residues: 28.9801
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  : 0.260 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 64 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9980
   chunk 76 optimal weight:    4.9990
   chunk 75 optimal weight:   10.0000
   chunk 77 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 59 optimal weight:    0.4980
   chunk 61 optimal weight:   10.0000
   chunk 63 optimal weight:    3.9990
   chunk 66 optimal weight:   10.0000
   overall best weight:    1.8984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 155 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.087389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.061622 restraints weight = 26995.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.3346 rms_B_bonded: 2.33
r_work: 0.3189 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.2398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9609  Z= 0.194
  Angle     :  0.590  11.102  13870  Z= 0.318
  Chirality :  0.038   0.201   1642
  Planarity :  0.004   0.044   1064
  Dihedral  : 16.990 107.143   2923
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 13.75 %
    Favored  : 83.99 %
  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 are not related in a simple way.
  whole:  1.39 (0.34), residues: 605
  helix:  2.39 (0.29), residues: 302
  sheet: -0.24 (0.39), residues: 134
  loop : -0.77 (0.45), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 242 
 TYR   0.021   0.001   TYR A 351 
 PHE   0.036   0.002   PHE A 253 
 TRP   0.011   0.001   TRP B  43 
 HIS   0.003   0.001   HIS A 278 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00399 /  0.19 ( 9605)
  covalent geometry    : angle       0.58515 /  0.32 (13864)
  hydrogen bonds       : bond        0.05300 /  3.25 (  459)
  hydrogen bonds       : angle       4.18390 /  3.07 ( 1170)
  metal coordination   : bond        0.00771 /  0.44 (    4)
  metal coordination   : angle       3.71586 /  2.28 (    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
  55 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 43
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7862 (mt-10)
REVERT: A  222 MET cc_start: 0.8487 (ttm) cc_final: 0.8131 (ttm)
REVERT: A  288 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8049 (mm-30)
REVERT: A  292 ASP cc_start: 0.8763 (m-30) cc_final: 0.8251 (m-30)
REVERT: B   26 GLN cc_start: 0.8140 (mm110) cc_final: 0.7685 (mm-40)
REVERT: B  137 MET cc_start: 0.6076 (mpp) cc_final: 0.5846 (mpm)
REVERT: B  156 GLU cc_start: 0.9033 (tm-30) cc_final: 0.8554 (tm-30)
REVERT: B  177 MET cc_start: 0.8613 (mmm) cc_final: 0.8384 (mmm)
  outliers start: 12
  outliers final: 8
  residues processed: 51
  average time/residue: 0.6600
  time to fit residues: 35.9702
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  : 0.300 
-------------------------------------------------------------------------------
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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 46 optimal weight:    7.9990
   chunk 6 optimal weight:    0.9980
   chunk 69 optimal weight:    8.9990
   chunk 35 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 44 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   overall best weight:    1.2582

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.088212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.062455 restraints weight = 26790.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.3366 rms_B_bonded: 2.33
r_work: 0.3209 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.2487

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= 0.157
  Angle     :  0.570  11.661  13870  Z= 0.308
  Chirality :  0.036   0.197   1642
  Planarity :  0.004   0.043   1064
  Dihedral  : 16.906 107.653   2923
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 14.50 %
    Favored  : 83.99 %
  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 are not related in a simple way.
  whole:  1.46 (0.34), residues: 605
  helix:  2.42 (0.29), residues: 302
  sheet: -0.19 (0.40), residues: 134
  loop : -0.70 (0.46), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 161 
 TYR   0.020   0.001   TYR A 351 
 PHE   0.040   0.002   PHE A 253 
 TRP   0.008   0.001   TRP B  43 
 HIS   0.003   0.001   HIS A 278 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00319 /  0.16 ( 9605)
  covalent geometry    : angle       0.56580 /  0.31 (13864)
  hydrogen bonds       : bond        0.05072 /  3.12 (  459)
  hydrogen bonds       : angle       4.11893 /  3.01 ( 1170)
  metal coordination   : bond        0.00614 /  0.35 (    4)
  metal coordination   : angle       3.42843 /  2.07 (    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
  51 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7847 (mt-10)
REVERT: A  222 MET cc_start: 0.8390 (ttm) cc_final: 0.8060 (ttm)
REVERT: A  288 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8009 (mm-30)
REVERT: A  292 ASP cc_start: 0.8754 (m-30) cc_final: 0.8239 (m-30)
REVERT: B   26 GLN cc_start: 0.8152 (mm110) cc_final: 0.7706 (mm-40)
REVERT: B  177 MET cc_start: 0.8577 (mmm) cc_final: 0.8348 (mmm)
  outliers start: 8
  outliers final: 8
  residues processed: 48
  average time/residue: 0.5481
  time to fit residues: 28.2684
Evaluate side-chains
  49 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 41
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 69 optimal weight:   10.0000
   chunk 72 optimal weight:    7.9990
   chunk 3 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 36 optimal weight:    0.3980
   chunk 55 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 45 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.7980

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.088876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.063209 restraints weight = 26736.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 2.30
r_work: 0.3235 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.2554

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= 0.140
  Angle     :  0.564  12.030  13870  Z= 0.305
  Chirality :  0.036   0.192   1642
  Planarity :  0.004   0.044   1064
  Dihedral  : 16.834 107.905   2923
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 14.69 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.58 (0.34), residues: 605
  helix:  2.50 (0.30), residues: 302
  sheet: -0.12 (0.40), residues: 132
  loop : -0.63 (0.46), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 136 
 TYR   0.020   0.001   TYR A 351 
 PHE   0.047   0.003   PHE A 253 
 TRP   0.011   0.001   TRP B  45 
 HIS   0.002   0.001   HIS A 303 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00286 /  0.14 ( 9605)
  covalent geometry    : angle       0.56000 /  0.30 (13864)
  hydrogen bonds       : bond        0.04913 /  3.03 (  459)
  hydrogen bonds       : angle       4.08386 /  2.98 ( 1170)
  metal coordination   : bond        0.00493 /  0.28 (    4)
  metal coordination   : angle       3.10812 /  1.86 (    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
  50 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7805 (mt-10)
REVERT: A  222 MET cc_start: 0.8313 (ttm) cc_final: 0.8011 (ttm)
REVERT: A  288 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8549 (tp30)
REVERT: A  292 ASP cc_start: 0.8745 (m-30) cc_final: 0.8504 (m-30)
REVERT: B   26 GLN cc_start: 0.8137 (mm110) cc_final: 0.7437 (mm-40)
REVERT: B   30 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7780 (mp0)
REVERT: B   46 MET cc_start: 0.8620 (mmm) cc_final: 0.8330 (mtp)
REVERT: B  106 GLN cc_start: 0.8074 (tt0) cc_final: 0.7753 (tt0)
REVERT: B  177 MET cc_start: 0.8581 (mmm) cc_final: 0.8359 (mmm)
  outliers start: 8
  outliers final: 7
  residues processed: 47
  average time/residue: 0.5212
  time to fit residues: 26.4181
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  : 0.250 
-------------------------------------------------------------------------------
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 69 optimal weight:   10.0000
   chunk 75 optimal weight:   10.0000
   chunk 28 optimal weight:    1.9990
   chunk 58 optimal weight:    9.9990
   chunk 15 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 62 optimal weight:    9.9990
   overall best weight:    1.7990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.087752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.062066 restraints weight = 26768.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.3359 rms_B_bonded: 2.33
r_work: 0.3202 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.2622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9609  Z= 0.192
  Angle     :  0.606  12.846  13870  Z= 0.321
  Chirality :  0.037   0.189   1642
  Planarity :  0.004   0.042   1064
  Dihedral  : 16.842 107.543   2923
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 11.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.52 (0.34), residues: 605
  helix:  2.46 (0.30), residues: 302
  sheet: -0.18 (0.40), residues: 131
  loop : -0.64 (0.46), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 136 
 TYR   0.021   0.001   TYR A 351 
 PHE   0.059   0.003   PHE A 253 
 TRP   0.010   0.001   TRP B  43 
 HIS   0.004   0.001   HIS A 278 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00399 /  0.19 ( 9605)
  covalent geometry    : angle       0.60286 /  0.32 (13864)
  hydrogen bonds       : bond        0.05183 /  3.19 (  459)
  hydrogen bonds       : angle       4.10992 /  3.00 ( 1170)
  metal coordination   : bond        0.00698 /  0.40 (    4)
  metal coordination   : angle       3.20823 /  1.95 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2989.33 seconds
wall clock time: 51 minutes 44.70 seconds (3104.70 seconds total)