Starting phenix.real_space_refine
on Sun Jun  8 02:03:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dzj_27801/06_2025/8dzj_27801.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dzj_27801/06_2025/8dzj_27801.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dzj_27801/06_2025/8dzj_27801.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dzj_27801/06_2025/8dzj_27801.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dzj_27801/06_2025/8dzj_27801.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dzj_27801/06_2025/8dzj_27801.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

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

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 9030
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3369
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 416, 3369
          Classifications: {'peptide': 416}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 405}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 1622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 197, 1622
          Classifications: {'peptide': 197}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 192}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "C"
      Number of atoms: 560
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 560
          Classifications: {'DNA': 27}
          Link IDs: {'rna3p': 26}
    Chain: "D"
      Number of atoms: 206
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 206
          Classifications: {'DNA': 10}
          Link IDs: {'rna3p': 9}
    Chain: "E"
      Number of atoms: 3272
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 153, 3272
          Classifications: {'RNA': 153}
          Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 5, 'rna3p_pur': 75, 'rna3p_pyr': 62}
          Link IDs: {'rna2p': 16, 'rna3p': 136}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

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

  Time building chain proxies: 6.77, per 1000 atoms: 0.75
  Number of scatterers: 9030
  At special positions: 0
  Unit cell: (85.2, 116.085, 137.385, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     S      21     16.00
     P     190     15.00
     O    2195      8.00
     N    1635      7.00
     C    4988      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.45
  Conformation dependent library (CDL) restraints added in 640.4 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: 4.51
  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: 4.95

  Time building geometry restraints manager: 2.94 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:             7.570
  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:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     33.560
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:31.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   72.840
-------------------------------------------------------------------------------
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 : 12.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  0.19 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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

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

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

*********************** 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  : 0.696 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 89
  average time/residue: 1.7571
  time to fit residues: 166.8018
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  : 0.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  326 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    9.9990
   chunk 59 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0270
   chunk 20 optimal weight:    0.5980
   chunk 39 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:   20.0000
   chunk 45 optimal weight:    4.9990
   chunk 70 optimal weight:    8.9990
   overall best weight:    1.1244

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.090274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.064627 restraints weight = 26567.209|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 2.26
r_work: 0.3265 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.1549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9609  Z= 0.151
  Angle     :  0.559   6.389  13870  Z= 0.298
  Chirality :  0.036   0.190   1642
  Planarity :  0.004   0.040   1064
  Dihedral  : 22.488 106.012   3433
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  :  9.60 %
    Favored  : 89.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.33), residues: 605
  helix:  2.29 (0.29), residues: 304
  sheet:  0.17 (0.41), residues: 134
  loop : -0.76 (0.44), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  45 
 HIS   0.006   0.001   HIS A 303 
 PHE   0.008   0.001   PHE B 102 
 TYR   0.024   0.001   TYR A 351 
 ARG   0.010   0.001   ARG A 242 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04875 (  459)
  hydrogen bonds       : angle       4.24262 ( 1170)
  metal coordination   : bond        0.00585 (    4)
  metal coordination   : angle       4.33956 (    6)
  covalent geometry    : bond        0.00317 ( 9605)
  covalent geometry    : angle       0.55189 (13864)

*********************** 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
  55 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 48
  time to evaluate  : 0.752 
Fit side-chains
   revert: symmetry clash
REVERT: A  222 MET cc_start: 0.8326 (ttm) cc_final: 0.7987 (ttt)
REVERT: A  288 GLU cc_start: 0.9130 (mm-30) cc_final: 0.8813 (mm-30)
REVERT: A  292 ASP cc_start: 0.8810 (m-30) cc_final: 0.8552 (m-30)
REVERT: B  155 GLN cc_start: 0.8917 (mm110) cc_final: 0.8696 (mm-40)
REVERT: B  156 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8500 (tm-30)
REVERT: B  177 MET cc_start: 0.8479 (mmm) cc_final: 0.8277 (mmm)
  outliers start: 7
  outliers final: 5
  residues processed: 53
  average time/residue: 1.2911
  time to fit residues: 73.6933
Evaluate side-chains
  45 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 40
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   66 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 35 optimal weight:    0.0570
   chunk 76 optimal weight:    6.9990
   chunk 63 optimal weight:    5.9990
   chunk 0 optimal weight:    3.9990
   chunk 14 optimal weight:    5.9990
   chunk 50 optimal weight:    1.9990
   chunk 46 optimal weight:    9.9990
   chunk 19 optimal weight:    8.9990
   chunk 18 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.9502

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.090360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.064735 restraints weight = 27072.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.3426 rms_B_bonded: 2.29
r_work: 0.3273 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.2009

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= 0.136
  Angle     :  0.542   7.585  13870  Z= 0.289
  Chirality :  0.035   0.176   1642
  Planarity :  0.004   0.040   1064
  Dihedral  : 22.379 106.733   3433
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 10.73 %
    Favored  : 87.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.34), residues: 605
  helix:  2.57 (0.29), residues: 304
  sheet:  0.10 (0.41), residues: 134
  loop : -0.66 (0.47), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  45 
 HIS   0.005   0.001   HIS A 303 
 PHE   0.009   0.001   PHE A 253 
 TYR   0.021   0.001   TYR A 351 
 ARG   0.006   0.000   ARG A 242 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04610 (  459)
  hydrogen bonds       : angle       4.06044 ( 1170)
  metal coordination   : bond        0.00534 (    4)
  metal coordination   : angle       3.65227 (    6)
  covalent geometry    : bond        0.00283 ( 9605)
  covalent geometry    : angle       0.53722 (13864)

*********************** 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
  51 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.749 
Fit side-chains
   revert: symmetry clash
REVERT: A  222 MET cc_start: 0.8230 (ttm) cc_final: 0.7808 (ttt)
REVERT: A  270 TYR cc_start: 0.4607 (t80) cc_final: 0.4152 (m-80)
REVERT: A  288 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8461 (tp30)
REVERT: A  292 ASP cc_start: 0.8899 (m-30) cc_final: 0.8500 (m-30)
REVERT: B   26 GLN cc_start: 0.8114 (mm110) cc_final: 0.7652 (mm-40)
REVERT: B  156 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8536 (tm-30)
REVERT: B  157 MET cc_start: 0.9104 (mmm) cc_final: 0.8828 (mpp)
REVERT: B  177 MET cc_start: 0.8574 (mmm) cc_final: 0.8273 (mmm)
  outliers start: 8
  outliers final: 4
  residues processed: 49
  average time/residue: 1.6735
  time to fit residues: 87.4647
Evaluate side-chains
  45 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 41
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   66 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 48 optimal weight:    6.9990
   chunk 38 optimal weight:    7.9990
   chunk 3 optimal weight:    3.9990
   chunk 57 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 36 optimal weight:    7.9990
   chunk 45 optimal weight:    4.9990
   chunk 41 optimal weight:    4.9990
   chunk 55 optimal weight:    0.8980
   chunk 58 optimal weight:    0.7980
   overall best weight:    1.7386

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.088290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.062486 restraints weight = 26795.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 2.30
r_work: 0.3211 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.2339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9609  Z= 0.189
  Angle     :  0.575   8.604  13870  Z= 0.304
  Chirality :  0.036   0.182   1642
  Planarity :  0.004   0.040   1064
  Dihedral  : 22.422 105.619   3431
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 11.68 %
    Favored  : 86.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.62 (0.34), residues: 605
  helix:  2.51 (0.29), residues: 302
  sheet:  0.01 (0.40), residues: 132
  loop : -0.66 (0.46), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  43 
 HIS   0.006   0.001   HIS A 303 
 PHE   0.016   0.002   PHE A 253 
 TYR   0.020   0.001   TYR A 351 
 ARG   0.006   0.000   ARG A 291 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05044 (  459)
  hydrogen bonds       : angle       4.12675 ( 1170)
  metal coordination   : bond        0.00766 (    4)
  metal coordination   : angle       3.55973 (    6)
  covalent geometry    : bond        0.00399 ( 9605)
  covalent geometry    : angle       0.57050 (13864)

*********************** 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
  50 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.678 
Fit side-chains
   revert: symmetry clash
REVERT: A  222 MET cc_start: 0.8407 (ttm) cc_final: 0.7993 (ttt)
REVERT: A  288 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8394 (tp30)
REVERT: A  292 ASP cc_start: 0.8898 (m-30) cc_final: 0.8528 (m-30)
REVERT: B   26 GLN cc_start: 0.8205 (mm110) cc_final: 0.7720 (mm-40)
REVERT: B  156 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8546 (tm-30)
REVERT: B  157 MET cc_start: 0.9128 (mmm) cc_final: 0.8868 (tpp)
REVERT: B  177 MET cc_start: 0.8566 (mmm) cc_final: 0.8360 (mmm)
  outliers start: 8
  outliers final: 4
  residues processed: 49
  average time/residue: 1.1712
  time to fit residues: 61.9340
Evaluate side-chains
  44 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   66 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 46 optimal weight:    9.9990
   chunk 74 optimal weight:    8.9990
   chunk 7 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 60 optimal weight:   10.0000
   chunk 21 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 28 optimal weight:    5.9990
   chunk 77 optimal weight:    8.9990
   chunk 27 optimal weight:    4.9990
   overall best weight:    2.1586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.086797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.061329 restraints weight = 27343.842|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 2.37
r_work: 0.3181 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.2697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   9609  Z= 0.218
  Angle     :  0.604  10.139  13870  Z= 0.319
  Chirality :  0.038   0.198   1642
  Planarity :  0.004   0.043   1064
  Dihedral  : 22.463 107.159   3431
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 12.05 %
    Favored  : 86.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.33), residues: 605
  helix:  2.37 (0.29), residues: 302
  sheet:  0.02 (0.41), residues: 132
  loop : -0.76 (0.44), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B  43 
 HIS   0.007   0.001   HIS A 303 
 PHE   0.021   0.002   PHE A 253 
 TYR   0.020   0.002   TYR A 351 
 ARG   0.005   0.001   ARG A 291 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05270 (  459)
  hydrogen bonds       : angle       4.18784 ( 1170)
  metal coordination   : bond        0.00889 (    4)
  metal coordination   : angle       4.21710 (    6)
  covalent geometry    : bond        0.00460 ( 9605)
  covalent geometry    : angle       0.59761 (13864)

*********************** 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  : 0.749 
Fit side-chains
   revert: symmetry clash
REVERT: A  222 MET cc_start: 0.8469 (ttm) cc_final: 0.8084 (ttm)
REVERT: A  288 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8350 (tp30)
REVERT: A  292 ASP cc_start: 0.8894 (m-30) cc_final: 0.8527 (m-30)
REVERT: B   26 GLN cc_start: 0.8221 (mm110) cc_final: 0.7687 (mm-40)
REVERT: B  156 GLU cc_start: 0.9061 (tm-30) cc_final: 0.8590 (tm-30)
REVERT: B  157 MET cc_start: 0.9068 (mmm) cc_final: 0.8843 (tpp)
  outliers start: 9
  outliers final: 8
  residues processed: 50
  average time/residue: 1.1824
  time to fit residues: 63.7344
Evaluate side-chains
  46 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 38
  time to evaluate  : 0.654 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 MET
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 45 optimal weight:    4.9990
   chunk 72 optimal weight:    7.9990
   chunk 27 optimal weight:    5.9990
   chunk 59 optimal weight:    0.9980
   chunk 13 optimal weight:    4.9990
   chunk 46 optimal weight:    0.5980
   chunk 10 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 71 optimal weight:    7.9990
   chunk 2 optimal weight:    0.9990
   overall best weight:    1.7186

-------------------------------------------------------------------------------
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 = 0.3963 r_free = 0.3963 target = 0.087332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.061833 restraints weight = 27231.265|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 2.33
r_work: 0.3195 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.2825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   9609  Z= 0.185
  Angle     :  0.588  10.840  13870  Z= 0.308
  Chirality :  0.036   0.195   1642
  Planarity :  0.004   0.037   1064
  Dihedral  : 22.395 107.397   3431
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 13.75 %
    Favored  : 84.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.34), residues: 605
  helix:  2.41 (0.29), residues: 302
  sheet: -0.03 (0.40), residues: 132
  loop : -0.63 (0.47), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  43 
 HIS   0.005   0.001   HIS A 303 
 PHE   0.024   0.002   PHE A 253 
 TYR   0.019   0.001   TYR A 351 
 ARG   0.004   0.000   ARG A 242 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05064 (  459)
  hydrogen bonds       : angle       4.12262 ( 1170)
  metal coordination   : bond        0.00788 (    4)
  metal coordination   : angle       3.85082 (    6)
  covalent geometry    : bond        0.00392 ( 9605)
  covalent geometry    : angle       0.58301 (13864)

*********************** 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
  50 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.757 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7803 (mt-10)
REVERT: A  222 MET cc_start: 0.8425 (ttm) cc_final: 0.8110 (ttm)
REVERT: A  288 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8381 (tp30)
REVERT: A  292 ASP cc_start: 0.8918 (m-30) cc_final: 0.8565 (m-30)
REVERT: B   26 GLN cc_start: 0.8180 (mm110) cc_final: 0.7665 (mm-40)
REVERT: B  156 GLU cc_start: 0.9062 (tm-30) cc_final: 0.8569 (tm-30)
REVERT: B  157 MET cc_start: 0.9022 (mmm) cc_final: 0.8820 (tpp)
  outliers start: 8
  outliers final: 6
  residues processed: 48
  average time/residue: 1.2231
  time to fit residues: 63.4934
Evaluate side-chains
  46 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.668 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 HIS
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain B residue    8 GLU
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   66 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 63 optimal weight:    5.9990
   chunk 67 optimal weight:   10.0000
   chunk 23 optimal weight:    5.9990
   chunk 0 optimal weight:    4.9990
   chunk 54 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 56 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 37 optimal weight:   20.0000
   chunk 27 optimal weight:    7.9990
   overall best weight:    3.3588

-------------------------------------------------------------------------------
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 = 0.3912 r_free = 0.3912 target = 0.084745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.059351 restraints weight = 27790.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 2.42
r_work: 0.3131 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.3114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.041   9609  Z= 0.313
  Angle     :  0.698  13.863  13870  Z= 0.363
  Chirality :  0.042   0.280   1642
  Planarity :  0.005   0.056   1064
  Dihedral  : 22.669 106.054   3431
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 13.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 13.94 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.33), residues: 605
  helix:  2.06 (0.29), residues: 302
  sheet: -0.19 (0.41), residues: 130
  loop : -0.87 (0.44), residues: 173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  43 
 HIS   0.007   0.002   HIS A 303 
 PHE   0.027   0.002   PHE A 253 
 TYR   0.018   0.002   TYR A 351 
 ARG   0.004   0.001   ARG B 136 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06153 (  459)
  hydrogen bonds       : angle       4.34497 ( 1170)
  metal coordination   : bond        0.01246 (    4)
  metal coordination   : angle       5.29612 (    6)
  covalent geometry    : bond        0.00662 ( 9605)
  covalent geometry    : angle       0.68936 (13864)

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

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

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

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.662 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7757 (mt-10)
REVERT: A  222 MET cc_start: 0.8627 (ttm) cc_final: 0.8250 (ttm)
REVERT: A  288 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8231 (tp30)
REVERT: A  292 ASP cc_start: 0.8901 (m-30) cc_final: 0.8548 (m-30)
REVERT: B   26 GLN cc_start: 0.8195 (mm110) cc_final: 0.7776 (mm-40)
REVERT: B  156 GLU cc_start: 0.9089 (tm-30) cc_final: 0.8037 (tm-30)
REVERT: B  157 MET cc_start: 0.9047 (mmm) cc_final: 0.8758 (mpp)
  outliers start: 11
  outliers final: 4
  residues processed: 51
  average time/residue: 1.3225
  time to fit residues: 72.1175
Evaluate side-chains
  44 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
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   66 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 64 optimal weight:    6.9990
   chunk 56 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 39 optimal weight:    5.9990
   chunk 76 optimal weight:    4.9990
   chunk 35 optimal weight:    0.0980
   chunk 43 optimal weight:    3.9990
   chunk 26 optimal weight:    9.9990
   chunk 38 optimal weight:    7.9990
   chunk 45 optimal weight:    4.9990
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
B 106 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.086764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.061380 restraints weight = 27883.773|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 2.36
r_work: 0.3187 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.3124

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= 0.181
  Angle     :  0.611  13.131  13870  Z= 0.317
  Chirality :  0.037   0.211   1642
  Planarity :  0.004   0.039   1064
  Dihedral  : 22.418 108.919   3431
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 14.50 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.34), residues: 605
  helix:  2.29 (0.29), residues: 302
  sheet: -0.10 (0.41), residues: 132
  loop : -0.74 (0.45), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  45 
 HIS   0.004   0.001   HIS A 278 
 PHE   0.034   0.002   PHE A 253 
 TYR   0.020   0.001   TYR A 351 
 ARG   0.004   0.000   ARG A 242 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05109 (  459)
  hydrogen bonds       : angle       4.17501 ( 1170)
  metal coordination   : bond        0.00776 (    4)
  metal coordination   : angle       4.29569 (    6)
  covalent geometry    : bond        0.00383 ( 9605)
  covalent geometry    : angle       0.60422 (13864)

*********************** 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
  56 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.866 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7786 (mt-10)
REVERT: A  222 MET cc_start: 0.8440 (ttm) cc_final: 0.8129 (ttm)
REVERT: A  292 ASP cc_start: 0.8911 (m-30) cc_final: 0.8610 (m-30)
REVERT: B   26 GLN cc_start: 0.8178 (mm110) cc_final: 0.7424 (mm-40)
REVERT: B   30 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7784 (mp0)
REVERT: B   46 MET cc_start: 0.8916 (mmm) cc_final: 0.8646 (mmm)
REVERT: B   66 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8500 (OUTLIER)
REVERT: B  156 GLU cc_start: 0.9086 (tm-30) cc_final: 0.8002 (tm-30)
  outliers start: 9
  outliers final: 9
  residues processed: 53
  average time/residue: 1.5034
  time to fit residues: 85.8350
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  : 0.822 
-------------------------------------------------------------------------------
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  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 14 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 69 optimal weight:    9.9990
   chunk 9 optimal weight:    0.9980
   chunk 22 optimal weight:    4.9990
   chunk 65 optimal weight:    5.9990
   chunk 53 optimal weight:    5.9990
   chunk 23 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   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 = 0.3942 r_free = 0.3942 target = 0.086021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.060631 restraints weight = 27546.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 2.42
r_work: 0.3169 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.3192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   9609  Z= 0.219
  Angle     :  0.649  13.783  13870  Z= 0.336
  Chirality :  0.038   0.202   1642
  Planarity :  0.004   0.044   1064
  Dihedral  : 22.423 107.876   3431
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 12.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 15.44 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.34), residues: 605
  helix:  2.29 (0.30), residues: 301
  sheet: -0.20 (0.41), residues: 131
  loop : -0.81 (0.44), residues: 173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  45 
 HIS   0.004   0.001   HIS A 278 
 PHE   0.043   0.002   PHE A 253 
 TYR   0.025   0.002   TYR A 270 
 ARG   0.003   0.000   ARG A 242 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05387 (  459)
  hydrogen bonds       : angle       4.21926 ( 1170)
  metal coordination   : bond        0.00905 (    4)
  metal coordination   : angle       4.33436 (    6)
  covalent geometry    : bond        0.00465 ( 9605)
  covalent geometry    : angle       0.64235 (13864)

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

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

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

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7793 (mt-10)
REVERT: A  222 MET cc_start: 0.8483 (ttm) cc_final: 0.8165 (ttm)
REVERT: A  292 ASP cc_start: 0.8909 (m-30) cc_final: 0.8615 (m-30)
REVERT: B   26 GLN cc_start: 0.8182 (mm110) cc_final: 0.7682 (mm-40)
REVERT: B   66 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8471 (OUTLIER)
REVERT: B  156 GLU cc_start: 0.9082 (tm-30) cc_final: 0.8784 (tm-30)
  outliers start: 9
  outliers final: 7
  residues processed: 49
  average time/residue: 1.3026
  time to fit residues: 68.3528
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  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  238 HIS
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  191 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 46 optimal weight:    0.1980
   chunk 6 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9980
   chunk 50 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 76 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 65 optimal weight:    9.9990
   chunk 0 optimal weight:    2.9990
   chunk 43 optimal weight:    5.9990
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 = 0.3983 r_free = 0.3983 target = 0.087998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.062787 restraints weight = 27340.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.3386 rms_B_bonded: 2.34
r_work: 0.3227 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.3287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9609  Z= 0.141
  Angle     :  0.595  13.132  13870  Z= 0.310
  Chirality :  0.035   0.197   1642
  Planarity :  0.004   0.040   1064
  Dihedral  : 22.305 108.314   3431
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 15.44 %
    Favored  : 83.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.52 (0.34), residues: 605
  helix:  2.43 (0.30), residues: 302
  sheet: -0.04 (0.42), residues: 131
  loop : -0.70 (0.45), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B  45 
 HIS   0.003   0.001   HIS A 278 
 PHE   0.044   0.002   PHE A 253 
 TYR   0.020   0.001   TYR A 351 
 ARG   0.004   0.000   ARG A 242 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04904 (  459)
  hydrogen bonds       : angle       4.13959 ( 1170)
  metal coordination   : bond        0.00554 (    4)
  metal coordination   : angle       3.61878 (    6)
  covalent geometry    : bond        0.00301 ( 9605)
  covalent geometry    : angle       0.59012 (13864)

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

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

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

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.805 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7755 (mt-10)
REVERT: A  222 MET cc_start: 0.8267 (ttm) cc_final: 0.7964 (ttm)
REVERT: A  288 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8363 (tp30)
REVERT: A  292 ASP cc_start: 0.8915 (m-30) cc_final: 0.8573 (m-30)
REVERT: B   26 GLN cc_start: 0.8093 (mm110) cc_final: 0.7518 (mm-40)
REVERT: B   46 MET cc_start: 0.8229 (mtp) cc_final: 0.7564 (ttm)
  outliers start: 8
  outliers final: 7
  residues processed: 48
  average time/residue: 1.9914
  time to fit residues: 102.8736
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  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  238 HIS
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  191 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 23 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 65 optimal weight:   10.9990
   chunk 19 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    1.0982

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.088064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.062519 restraints weight = 27503.029|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 2.39
r_work: 0.3221 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.3375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9609  Z= 0.151
  Angle     :  0.613  15.016  13870  Z= 0.318
  Chirality :  0.036   0.203   1642
  Planarity :  0.004   0.039   1064
  Dihedral  : 22.257 107.471   3431
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 15.25 %
    Favored  : 83.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.34), residues: 605
  helix:  2.45 (0.30), residues: 301
  sheet: -0.06 (0.42), residues: 130
  loop : -0.75 (0.45), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  45 
 HIS   0.003   0.001   HIS A 278 
 PHE   0.052   0.002   PHE A 253 
 TYR   0.024   0.001   TYR A 270 
 ARG   0.004   0.000   ARG A 242 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04955 (  459)
  hydrogen bonds       : angle       4.12144 ( 1170)
  metal coordination   : bond        0.00553 (    4)
  metal coordination   : angle       3.38231 (    6)
  covalent geometry    : bond        0.00325 ( 9605)
  covalent geometry    : angle       0.60859 (13864)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7740.91 seconds
wall clock time: 137 minutes 40.32 seconds (8260.32 seconds total)