Starting phenix.real_space_refine
on Thu Jul 24 16:24:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y7z_39027/07_2025/8y7z_39027.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y7z_39027/07_2025/8y7z_39027.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y7z_39027/07_2025/8y7z_39027.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y7z_39027/07_2025/8y7z_39027.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y7z_39027/07_2025/8y7z_39027.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y7z_39027/07_2025/8y7z_39027.cif"
  }
  resolution = 2.57
  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=  -0.001 sd=   0.098
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
     P      41      5.49       5
     Mg      1      5.21       5
     S      22      5.16       5
     C    4007      2.51       5
     N    1117      2.21       5
     O    1300      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6488
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 3629
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 456, 3629
          Classifications: {'peptide': 456}
          Link IDs: {'PTRANS': 27, 'TRANS': 428}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 2005
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 252, 2005
          Classifications: {'peptide': 252}
          Link IDs: {'PTRANS': 9, 'TRANS': 242}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 442
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 442
          Classifications: {'RNA': 21}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 10}
          Link IDs: {'rna2p': 2, 'rna3p': 18}
    Chain: "D"
      Number of atoms: 411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 411
          Classifications: {'DNA': 20}
          Link IDs: {'rna3p': 19}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 7.05, per 1000 atoms: 1.09
  Number of scatterers: 6488
  At special positions: 0
  Unit cell: (68.641, 79.392, 106.683, 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)
     S      22     16.00
     P      41     15.00
     Mg      1     11.99
     O    1300      8.00
     N    1117      7.00
     C    4007      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: 1.80
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1326

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 11 sheets defined
      37.6% alpha, 24.3% beta
      15 base pairs and 30 stacking pairs defined.
    Time for finding SS restraints: 3.79
  Creating SS restraints...
    Processing helix  chain 'B' and resid 29 through 38
    Processing helix  chain 'B' and resid 39 through 43
      removed outlier: 3.847A  pdb=" N   CYS B  43 " --> pdb=" O   TYR B  40 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 60 through 73
      removed outlier: 3.618A  pdb=" N   LEU B  64 " --> pdb=" O   HIS B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 89 through 95
    Processing helix  chain 'B' and resid 102 through 104
      No H-bonds generated for 'chain 'B' and resid 102 through 104'
    Processing helix  chain 'B' and resid 110 through 119
      removed outlier: 3.826A  pdb=" N   HIS B 114 " --> pdb=" O   LEU B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 132
    Processing helix  chain 'B' and resid 133 through 139
      removed outlier: 3.788A  pdb=" N   ARG B 138 " --> pdb=" O   SER B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 151 through 157
      removed outlier: 4.769A  pdb=" N   LYS B 156 " --> pdb=" O   SER B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 165 through 173
    Processing helix  chain 'B' and resid 184 through 190
      removed outlier: 3.966A  pdb=" N   LEU B 188 " --> pdb=" O   ASN B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 208
      removed outlier: 3.834A  pdb=" N   VAL B 196 " --> pdb=" O   CYS B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 294
      removed outlier: 3.550A  pdb=" N   SER B 282 " --> pdb=" O   GLN B 278 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   SER B 294 " --> pdb=" O   LEU B 290 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 312 through 323
      removed outlier: 3.719A  pdb=" N   PHE B 323 " --> pdb=" O   ALA B 319 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 428
      removed outlier: 4.717A  pdb=" N   THR B 421 " --> pdb=" O   GLY B 417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 459
    Processing helix  chain 'B' and resid 470 through 472
      No H-bonds generated for 'chain 'B' and resid 470 through 472'
    Processing helix  chain 'A' and resid 355 through 367
    Processing helix  chain 'A' and resid 383 through 391
      removed outlier: 3.555A  pdb=" N   ILE A 387 " --> pdb=" O   GLY A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 414
    Processing helix  chain 'A' and resid 414 through 430
    Processing helix  chain 'A' and resid 455 through 457
      No H-bonds generated for 'chain 'A' and resid 455 through 457'
    Processing helix  chain 'A' and resid 458 through 466
    Processing helix  chain 'A' and resid 513 through 519
      removed outlier: 4.878A  pdb=" N   GLU A 518 " --> pdb=" O   ASP A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 529
    Processing helix  chain 'A' and resid 532 through 549
    Processing sheet with id=AA1, first strand: chain 'B' and resid 12 through 13
      removed outlier: 6.401A  pdb=" N   ILE B 303 " --> pdb=" O   GLU B 330 " (cutoff:3.500A)
      removed outlier: 7.335A  pdb=" N   VAL B 332 " --> pdb=" O   ILE B 303 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   ILE B 305 " --> pdb=" O   VAL B 332 " (cutoff:3.500A)
      removed outlier: 7.209A  pdb=" N   ILE B 334 " --> pdb=" O   ILE B 305 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   LYS B 307 " --> pdb=" O   ILE B 334 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   ALA B 223 " --> pdb=" O   PHE B 304 " (cutoff:3.500A)
      removed outlier: 7.789A  pdb=" N   HIS B 306 " --> pdb=" O   ALA B 223 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   ILE B 225 " --> pdb=" O   HIS B 306 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 25 through 27
      removed outlier: 3.533A  pdb=" N   ARG B  25 " --> pdb=" O   PHE B  21 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 98 through 99
      removed outlier: 8.493A  pdb=" N   CYS B 107 " --> pdb=" O   LEU B  52 " (cutoff:3.500A)
      removed outlier: 5.863A  pdb=" N   TYR B  54 " --> pdb=" O   CYS B 107 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 98 through 99
      removed outlier: 6.407A  pdb=" N   ARG B  51 " --> pdb=" O   VAL B 145 " (cutoff:3.500A)
      removed outlier: 7.209A  pdb=" N   LEU B 147 " --> pdb=" O   ARG B  51 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   ALA B  53 " --> pdb=" O   LEU B 147 " (cutoff:3.500A)
      removed outlier: 7.555A  pdb=" N   TYR B 149 " --> pdb=" O   ALA B  53 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   LEU B  55 " --> pdb=" O   TYR B 149 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   LEU B 146 " --> pdb=" O   GLN B 181 " (cutoff:3.500A)
      removed outlier: 7.343A  pdb=" N   ILE B 183 " --> pdb=" O   LEU B 146 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   VAL B 148 " --> pdb=" O   ILE B 183 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 159 through 160
      removed outlier: 3.544A  pdb=" N   TYR B 160 " --> pdb=" O   PHE B 163 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 343 through 344
    Processing sheet with id=AA7, first strand: chain 'B' and resid 381 through 382
    Processing sheet with id=AA8, first strand: chain 'A' and resid 335 through 337
      removed outlier: 4.017A  pdb=" N   HIS A 444 " --> pdb=" O   ILE A 492 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 335 through 337
    Processing sheet with id=AB1, first strand: chain 'A' and resid 370 through 373
      removed outlier: 7.031A  pdb=" N   GLY A 382 " --> pdb=" O   ARG A 344 " (cutoff:3.500A)
      removed outlier: 10.649A  pdb=" N   ARG A 344 " --> pdb=" O   GLY A 382 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   ILE A 343 " --> pdb=" O   TYR A 403 " (cutoff:3.500A)
      removed outlier: 4.971A  pdb=" N   TYR A 403 " --> pdb=" O   ILE A 343 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   CYS A 345 " --> pdb=" O   GLN A 401 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   GLN A 401 " --> pdb=" O   CYS A 345 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   VAL A 347 " --> pdb=" O   ILE A 399 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   ILE A 399 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   THR A 349 " --> pdb=" O   ASN A 397 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 558 through 561
      removed outlier: 3.560A  pdb=" N   ALA A 569 " --> pdb=" O   CYS A 561 " (cutoff:3.500A)

    250 hydrogen bonds defined for protein.
    684 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      35 hydrogen bonds
      62 hydrogen bond angles
      0 basepair planarities
      15 basepair parallelities
      30 stacking parallelities
  Total time for adding SS restraints: 3.02

  Time building geometry restraints manager: 2.15 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1866
        1.34 -     1.45: 1407
        1.45 -     1.57: 3336
        1.57 -     1.69: 81
        1.69 -     1.81: 32
  Bond restraints: 6722
  Sorted by residual:
  bond pdb=" CA  ASN B 121 "
       pdb=" CB  ASN B 121 "
    ideal  model  delta    sigma   weight residual
    1.531  1.579 -0.049 3.28e-02 9.30e+02 2.21e+00
  bond pdb=" C3'  DA D  18 "
       pdb=" O3'  DA D  18 "
    ideal  model  delta    sigma   weight residual
    1.422  1.459 -0.037 3.00e-02 1.11e+03 1.52e+00
  bond pdb=" C3'  DT D  23 "
       pdb=" O3'  DT D  23 "
    ideal  model  delta    sigma   weight residual
    1.422  1.458 -0.036 3.00e-02 1.11e+03 1.41e+00
  bond pdb=" CB  ASN B 296 "
       pdb=" CG  ASN B 296 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 2.50e-02 1.60e+03 1.06e+00
  bond pdb=" CG  LEU B 288 "
       pdb=" CD2 LEU B 288 "
    ideal  model  delta    sigma   weight residual
    1.521  1.489  0.032 3.30e-02 9.18e+02 9.55e-01
  ... (remaining 6717 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.78: 9046
        1.78 -     3.55: 215
        3.55 -     5.33: 24
        5.33 -     7.11: 6
        7.11 -     8.88: 2
  Bond angle restraints: 9293
  Sorted by residual:
  angle pdb=" CB  MET B 383 "
        pdb=" CG  MET B 383 "
        pdb=" SD  MET B 383 "
      ideal   model   delta    sigma   weight residual
     112.70  121.58   -8.88 3.00e+00 1.11e-01 8.77e+00
  angle pdb=" O4'  DT D  12 "
        pdb=" C1'  DT D  12 "
        pdb=" N1   DT D  12 "
      ideal   model   delta    sigma   weight residual
     108.40  112.58   -4.18 1.50e+00 4.44e-01 7.77e+00
  angle pdb=" C   HIS A 441 "
        pdb=" CA  HIS A 441 "
        pdb=" CB  HIS A 441 "
      ideal   model   delta    sigma   weight residual
     110.42  115.96   -5.54 1.99e+00 2.53e-01 7.75e+00
  angle pdb=" N   GLY B 209 "
        pdb=" CA  GLY B 209 "
        pdb=" C   GLY B 209 "
      ideal   model   delta    sigma   weight residual
     113.18  107.21    5.97 2.37e+00 1.78e-01 6.34e+00
  angle pdb=" N   HIS A 441 "
        pdb=" CA  HIS A 441 "
        pdb=" C   HIS A 441 "
      ideal   model   delta    sigma   weight residual
     110.80  105.57    5.23 2.13e+00 2.20e-01 6.02e+00
  ... (remaining 9288 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.78: 3680
       32.78 -    65.56: 299
       65.56 -    98.34: 20
       98.34 -   131.13: 0
      131.13 -   163.91: 2
  Dihedral angle restraints: 4001
    sinusoidal: 1942
      harmonic: 2059
  Sorted by residual:
  dihedral pdb=" CA  LEU B  46 "
           pdb=" C   LEU B  46 "
           pdb=" N   PRO B  47 "
           pdb=" CA  PRO B  47 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.12   22.88     0      5.00e+00 4.00e-02 2.09e+01
  dihedral pdb=" C4'  DT D  23 "
           pdb=" C3'  DT D  23 "
           pdb=" O3'  DT D  23 "
           pdb=" P    DA D  24 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   56.09  163.91     1      3.50e+01 8.16e-04 1.54e+01
  dihedral pdb=" C4'  DA D  18 "
           pdb=" C3'  DA D  18 "
           pdb=" O3'  DA D  18 "
           pdb=" P    DG D  19 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   65.62  154.38     1      3.50e+01 8.16e-04 1.49e+01
  ... (remaining 3998 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 756
       0.040 -    0.080: 205
       0.080 -    0.120: 70
       0.120 -    0.160: 14
       0.160 -    0.200: 2
  Chirality restraints: 1047
  Sorted by residual:
  chirality pdb=" CB  VAL B 247 "
            pdb=" CA  VAL B 247 "
            pdb=" CG1 VAL B 247 "
            pdb=" CG2 VAL B 247 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 1.00e+00
  chirality pdb=" C1'   A C  20 "
            pdb=" O4'   A C  20 "
            pdb=" C2'   A C  20 "
            pdb=" N9    A C  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.28    0.18 2.00e-01 2.50e+01 7.77e-01
  chirality pdb=" CB  ILE B 225 "
            pdb=" CA  ILE B 225 "
            pdb=" CG1 ILE B 225 "
            pdb=" CG2 ILE B 225 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.15 2.00e-01 2.50e+01 5.85e-01
  ... (remaining 1044 not shown)

  Planarity restraints: 1043
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT D  12 "   -0.027 2.00e-02 2.50e+03   1.44e-02 5.21e+00
        pdb=" N1   DT D  12 "    0.036 2.00e-02 2.50e+03
        pdb=" C2   DT D  12 "    0.002 2.00e-02 2.50e+03
        pdb=" O2   DT D  12 "    0.000 2.00e-02 2.50e+03
        pdb=" N3   DT D  12 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4   DT D  12 "   -0.004 2.00e-02 2.50e+03
        pdb=" O4   DT D  12 "   -0.006 2.00e-02 2.50e+03
        pdb=" C5   DT D  12 "   -0.001 2.00e-02 2.50e+03
        pdb=" C7   DT D  12 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6   DT D  12 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C C   5 "    0.026 2.00e-02 2.50e+03   1.38e-02 4.31e+00
        pdb=" N1    C C   5 "   -0.030 2.00e-02 2.50e+03
        pdb=" C2    C C   5 "    0.000 2.00e-02 2.50e+03
        pdb=" O2    C C   5 "   -0.004 2.00e-02 2.50e+03
        pdb=" N3    C C   5 "    0.002 2.00e-02 2.50e+03
        pdb=" C4    C C   5 "    0.003 2.00e-02 2.50e+03
        pdb=" N4    C C   5 "    0.007 2.00e-02 2.50e+03
        pdb=" C5    C C   5 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6    C C   5 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C C   4 "   -0.027 2.00e-02 2.50e+03   1.35e-02 4.11e+00
        pdb=" N1    C C   4 "    0.027 2.00e-02 2.50e+03
        pdb=" C2    C C   4 "    0.005 2.00e-02 2.50e+03
        pdb=" O2    C C   4 "    0.003 2.00e-02 2.50e+03
        pdb=" N3    C C   4 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    C C   4 "   -0.003 2.00e-02 2.50e+03
        pdb=" N4    C C   4 "   -0.010 2.00e-02 2.50e+03
        pdb=" C5    C C   4 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    C C   4 "    0.006 2.00e-02 2.50e+03
  ... (remaining 1040 not shown)

  Histogram of nonbonded interaction distances:
        1.96 -     2.55: 57
        2.55 -     3.13: 4821
        3.13 -     3.72: 11324
        3.72 -     4.31: 16395
        4.31 -     4.90: 25575
  Nonbonded interactions: 58172
  Sorted by model distance:
  nonbonded pdb=" OP1   A C   1 "
            pdb="MG    MG B 501 "
     model   vdw
     1.958 2.170
  nonbonded pdb=" ND2 ASN B 434 "
            pdb="MG    MG B 501 "
     model   vdw
     2.059 2.250
  nonbonded pdb=" N2    G C  11 "
            pdb=" O2   DC D  13 "
     model   vdw
     2.138 2.496
  nonbonded pdb=" O   THR B 242 "
            pdb=" OG1 THR B 262 "
     model   vdw
     2.142 3.040
  nonbonded pdb=" N2    G C  16 "
            pdb=" O2   DC D   8 "
     model   vdw
     2.147 2.496
  ... (remaining 58167 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:             117.670
  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:             0.000
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     27.260
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:17.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  162.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   6722  Z= 0.168
  Angle     :  0.657   8.885   9293  Z= 0.352
  Chirality :  0.043   0.200   1047
  Planarity :  0.004   0.042   1043
  Dihedral  : 20.761 163.906   2675
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 14.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  : 28.62 %
    Favored  : 71.05 %
  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: -0.35 (0.32), residues: 698
  helix:  0.40 (0.35), residues: 217
  sheet: -0.45 (0.38), residues: 166
  loop : -0.41 (0.37), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 198 
 HIS   0.003   0.001   HIS B 166 
 PHE   0.012   0.002   PHE B 257 
 TYR   0.021   0.002   TYR B  84 
 ARG   0.008   0.000   ARG B 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08523 (  269)
  hydrogen bonds       : angle       5.44428 (  746)
  covalent geometry    : bond        0.00373 ( 6722)
  covalent geometry    : angle       0.65739 ( 9293)

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 83
  time to evaluate  : 0.953 
Fit side-chains
REVERT: B  299 MET cc_start: 0.7363 (mmt) cc_final: 0.6900 (mmm)
REVERT: A  508 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6826 (mm-30)
  outliers start: 2
  outliers final: 1
  residues processed: 85
  average time/residue: 1.5518
  time to fit residues: 139.5086
Evaluate side-chains
  75 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 74
  time to evaluate  : 1.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  247 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 62 optimal weight:    0.6980
   chunk 56 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0020
   chunk 29 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 43 optimal weight:    0.5980
   chunk 67 optimal weight:    3.9990
   overall best weight:    0.5988

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

Flipped N/Q/H residues before XYZ refinement:
** B  29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 409 GLN
A 437 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.171138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.141642 restraints weight = 5760.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.3725 rms_B_bonded: 1.44
r_work: 0.3622 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3514 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.0625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6722  Z= 0.165
  Angle     :  0.616   8.457   9293  Z= 0.324
  Chirality :  0.042   0.170   1047
  Planarity :  0.005   0.040   1043
  Dihedral  : 19.479 164.118   1326
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 27.30 %
    Favored  : 68.59 %
  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: -0.24 (0.32), residues: 698
  helix:  0.45 (0.34), residues: 217
  sheet: -0.46 (0.39), residues: 165
  loop : -0.26 (0.37), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 198 
 HIS   0.004   0.001   HIS B  60 
 PHE   0.016   0.002   PHE B 255 
 TYR   0.017   0.002   TYR B  84 
 ARG   0.006   0.001   ARG B 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05416 (  269)
  hydrogen bonds       : angle       5.24398 (  746)
  covalent geometry    : bond        0.00372 ( 6722)
  covalent geometry    : angle       0.61623 ( 9293)

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 82
  time to evaluate  : 1.936 
Fit side-chains
   revert: symmetry clash
REVERT: B  315 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7320 (mt-10)
REVERT: B  383 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7662 (mmm)
REVERT: A  484 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7977 (tp)
REVERT: A  508 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7176 (mm-30)
  outliers start: 25
  outliers final: 9
  residues processed: 100
  average time/residue: 2.0863
  time to fit residues: 219.9139
Evaluate side-chains
  85 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 74
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  341 TYR
Chi-restraints excluded: chain B residue  343 LEU
Chi-restraints excluded: chain B residue  383 MET
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  466 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  484 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 69 optimal weight:    0.0870
   chunk 14 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 66 optimal weight:    0.7980
   chunk 51 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 25 optimal weight:    4.9990
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
** B  29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 409 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.170275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.140963 restraints weight = 5778.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.3716 rms_B_bonded: 1.42
r_work: 0.3612 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3507 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.0865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6722  Z= 0.168
  Angle     :  0.606   8.379   9293  Z= 0.319
  Chirality :  0.042   0.166   1047
  Planarity :  0.004   0.039   1043
  Dihedral  : 19.377 164.568   1326
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 26.48 %
    Favored  : 68.59 %
  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: -0.22 (0.32), residues: 698
  helix:  0.47 (0.34), residues: 218
  sheet: -0.42 (0.39), residues: 165
  loop : -0.27 (0.37), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 198 
 HIS   0.004   0.001   HIS B  60 
 PHE   0.014   0.002   PHE B 255 
 TYR   0.016   0.002   TYR B  84 
 ARG   0.010   0.001   ARG B 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05371 (  269)
  hydrogen bonds       : angle       5.18489 (  746)
  covalent geometry    : bond        0.00378 ( 6722)
  covalent geometry    : angle       0.60621 ( 9293)

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 78
  time to evaluate  : 1.001 
Fit side-chains
REVERT: B  315 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7328 (mt-10)
REVERT: A  484 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8011 (tp)
REVERT: A  508 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7180 (mm-30)
REVERT: A  528 ARG cc_start: 0.7189 (ttp-170) cc_final: 0.6383 (ttt180)
  outliers start: 30
  outliers final: 14
  residues processed: 100
  average time/residue: 1.9877
  time to fit residues: 210.9228
Evaluate side-chains
  87 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 2.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  127 ASP
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain B residue  239 GLU
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  341 TYR
Chi-restraints excluded: chain B residue  343 LEU
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  466 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  484 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 66 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0970
   chunk 64 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 39 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 1 optimal weight:    0.7980
   chunk 6 optimal weight:    0.3980
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
** B  29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 409 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.172091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.142964 restraints weight = 5828.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.3737 rms_B_bonded: 1.43
r_work: 0.3635 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3529 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.1006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6722  Z= 0.146
  Angle     :  0.586   8.175   9293  Z= 0.307
  Chirality :  0.041   0.157   1047
  Planarity :  0.004   0.039   1043
  Dihedral  : 19.297 164.443   1326
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 26.81 %
    Favored  : 68.26 %
  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: -0.08 (0.32), residues: 698
  helix:  0.69 (0.35), residues: 217
  sheet: -0.43 (0.39), residues: 169
  loop : -0.21 (0.38), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 198 
 HIS   0.003   0.001   HIS B  60 
 PHE   0.013   0.002   PHE B 255 
 TYR   0.020   0.002   TYR B  84 
 ARG   0.011   0.001   ARG B 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05264 (  269)
  hydrogen bonds       : angle       5.06682 (  746)
  covalent geometry    : bond        0.00328 ( 6722)
  covalent geometry    : angle       0.58581 ( 9293)

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 81
  time to evaluate  : 0.751 
Fit side-chains
REVERT: B  100 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7682 (mtp)
REVERT: B  289 HIS cc_start: 0.7550 (t70) cc_final: 0.7264 (t70)
REVERT: B  298 ARG cc_start: 0.6699 (ttp-110) cc_final: 0.6345 (mtp180)
REVERT: B  315 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7288 (mt-10)
REVERT: B  330 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6983 (tp30)
REVERT: A  484 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7970 (tp)
REVERT: A  508 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7224 (mm-30)
REVERT: A  512 LYS cc_start: 0.6915 (OUTLIER) cc_final: 0.6416 (tmtp)
REVERT: A  528 ARG cc_start: 0.7176 (ttp-170) cc_final: 0.6434 (ptt180)
  outliers start: 30
  outliers final: 16
  residues processed: 102
  average time/residue: 1.2588
  time to fit residues: 135.0727
Evaluate side-chains
  95 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 75
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  100 MET
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain B residue  239 GLU
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  330 GLU
Chi-restraints excluded: chain B residue  341 TYR
Chi-restraints excluded: chain B residue  343 LEU
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  421 THR
Chi-restraints excluded: chain B residue  466 ILE
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain A residue  512 LYS
Chi-restraints excluded: chain A residue  514 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 36 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 52 optimal weight:    0.0060
   chunk 2 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 62 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.6798

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

Flipped N/Q/H residues before XYZ refinement:
** B  29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 409 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.170242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.140853 restraints weight = 5805.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.3715 rms_B_bonded: 1.43
r_work: 0.3609 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3504 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.1079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6722  Z= 0.170
  Angle     :  0.604   8.630   9293  Z= 0.315
  Chirality :  0.042   0.152   1047
  Planarity :  0.004   0.045   1043
  Dihedral  : 19.278 164.892   1326
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 26.64 %
    Favored  : 68.26 %
  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: -0.11 (0.32), residues: 698
  helix:  0.65 (0.34), residues: 217
  sheet: -0.42 (0.39), residues: 169
  loop : -0.23 (0.38), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 510 
 HIS   0.003   0.001   HIS B 166 
 PHE   0.017   0.002   PHE B 255 
 TYR   0.023   0.002   TYR B  84 
 ARG   0.010   0.001   ARG B 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05327 (  269)
  hydrogen bonds       : angle       5.06964 (  746)
  covalent geometry    : bond        0.00383 ( 6722)
  covalent geometry    : angle       0.60423 ( 9293)

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 79
  time to evaluate  : 0.693 
Fit side-chains
REVERT: B   51 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7953 (mtm-85)
REVERT: B  298 ARG cc_start: 0.6773 (ttp-110) cc_final: 0.6438 (mtp180)
REVERT: B  330 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.6965 (tp30)
REVERT: A  484 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7973 (tp)
REVERT: A  508 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7228 (mm-30)
  outliers start: 31
  outliers final: 18
  residues processed: 103
  average time/residue: 1.1693
  time to fit residues: 127.1429
Evaluate side-chains
  98 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 77
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 ARG
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  127 ASP
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain B residue  239 GLU
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  330 GLU
Chi-restraints excluded: chain B residue  341 TYR
Chi-restraints excluded: chain B residue  343 LEU
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  421 THR
Chi-restraints excluded: chain B residue  466 ILE
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  484 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0980
   chunk 41 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 63 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0370
   chunk 54 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.4860

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

Flipped N/Q/H residues before XYZ refinement:
** B  29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 409 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.172186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.143180 restraints weight = 5723.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.3741 rms_B_bonded: 1.42
r_work: 0.3639 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3534 rms_B_bonded: 3.11 restraints_weight: 0.2500
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.1171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6722  Z= 0.145
  Angle     :  0.584   8.477   9293  Z= 0.306
  Chirality :  0.041   0.153   1047
  Planarity :  0.004   0.046   1043
  Dihedral  : 19.256 164.556   1326
  Min Nonbonded Distance : 1.967

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 27.30 %
    Favored  : 67.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.04 (0.32), residues: 698
  helix:  0.74 (0.35), residues: 218
  sheet: -0.40 (0.39), residues: 169
  loop : -0.21 (0.38), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 198 
 HIS   0.003   0.001   HIS B 166 
 PHE   0.017   0.002   PHE B 257 
 TYR   0.023   0.002   TYR B  84 
 ARG   0.011   0.000   ARG B 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05236 (  269)
  hydrogen bonds       : angle       4.99304 (  746)
  covalent geometry    : bond        0.00329 ( 6722)
  covalent geometry    : angle       0.58435 ( 9293)

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 83
  time to evaluate  : 0.631 
Fit side-chains
REVERT: B   51 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7945 (mtm-85)
REVERT: B  110 LEU cc_start: 0.7664 (mp) cc_final: 0.7455 (mp)
REVERT: B  289 HIS cc_start: 0.7538 (t70) cc_final: 0.7247 (t70)
REVERT: B  307 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8011 (tttp)
REVERT: B  330 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6958 (tp30)
REVERT: A  367 SER cc_start: 0.7923 (m) cc_final: 0.7243 (p)
REVERT: A  484 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7940 (tp)
REVERT: A  508 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7170 (mm-30)
REVERT: A  512 LYS cc_start: 0.6909 (OUTLIER) cc_final: 0.6433 (tmtp)
REVERT: A  528 ARG cc_start: 0.7176 (ttp-170) cc_final: 0.6452 (ptt180)
  outliers start: 32
  outliers final: 19
  residues processed: 106
  average time/residue: 1.1800
  time to fit residues: 131.6828
Evaluate side-chains
  100 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 76
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 ARG
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  127 ASP
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  307 LYS
Chi-restraints excluded: chain B residue  330 GLU
Chi-restraints excluded: chain B residue  341 TYR
Chi-restraints excluded: chain B residue  343 LEU
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  403 LEU
Chi-restraints excluded: chain B residue  421 THR
Chi-restraints excluded: chain B residue  466 ILE
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain A residue  512 LYS
Chi-restraints excluded: chain A residue  514 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 31 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 57 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 64 optimal weight:    2.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
** B  29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 281 GLN
A 409 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.165269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.135468 restraints weight = 5742.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.3657 rms_B_bonded: 1.44
r_work: 0.3552 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3442 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.1243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   6722  Z= 0.288
  Angle     :  0.712   8.504   9293  Z= 0.370
  Chirality :  0.046   0.180   1047
  Planarity :  0.005   0.045   1043
  Dihedral  : 19.333 165.652   1326
  Min Nonbonded Distance : 1.903

Molprobity Statistics.
  All-atom Clashscore : 12.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 26.81 %
    Favored  : 67.76 %
  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: -0.41 (0.31), residues: 698
  helix:  0.24 (0.33), residues: 216
  sheet: -0.49 (0.40), residues: 165
  loop : -0.34 (0.36), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 510 
 HIS   0.006   0.001   HIS B 166 
 PHE   0.020   0.003   PHE B 257 
 TYR   0.028   0.002   TYR B  84 
 ARG   0.012   0.001   ARG B 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05997 (  269)
  hydrogen bonds       : angle       5.34004 (  746)
  covalent geometry    : bond        0.00649 ( 6722)
  covalent geometry    : angle       0.71202 ( 9293)

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 78
  time to evaluate  : 0.650 
Fit side-chains
REVERT: B  185 ASP cc_start: 0.7599 (m-30) cc_final: 0.7389 (m-30)
REVERT: B  222 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6489 (mm-30)
REVERT: B  298 ARG cc_start: 0.6750 (ttp-110) cc_final: 0.6407 (mtp180)
REVERT: B  307 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8175 (tttp)
REVERT: A  367 SER cc_start: 0.7959 (m) cc_final: 0.7304 (p)
REVERT: A  484 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8023 (tp)
  outliers start: 33
  outliers final: 17
  residues processed: 102
  average time/residue: 1.2176
  time to fit residues: 130.6543
Evaluate side-chains
  92 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 72
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  127 ASP
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain B residue  222 GLU
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  307 LYS
Chi-restraints excluded: chain B residue  330 GLU
Chi-restraints excluded: chain B residue  341 TYR
Chi-restraints excluded: chain B residue  343 LEU
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  421 THR
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  466 ILE
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  484 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 13 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** B  29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 281 GLN
A 409 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.168124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.138453 restraints weight = 5753.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.3689 rms_B_bonded: 1.43
r_work: 0.3586 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3478 rms_B_bonded: 3.11 restraints_weight: 0.2500
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.1210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6722  Z= 0.198
  Angle     :  0.642   8.455   9293  Z= 0.336
  Chirality :  0.043   0.154   1047
  Planarity :  0.005   0.052   1043
  Dihedral  : 19.290 164.825   1326
  Min Nonbonded Distance : 1.933

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 27.63 %
    Favored  : 67.60 %
  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: -0.32 (0.32), residues: 698
  helix:  0.42 (0.34), residues: 218
  sheet: -0.58 (0.40), residues: 165
  loop : -0.29 (0.37), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 510 
 HIS   0.003   0.001   HIS B 166 
 PHE   0.021   0.002   PHE B 255 
 TYR   0.026   0.002   TYR B  84 
 ARG   0.012   0.001   ARG B 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05460 (  269)
  hydrogen bonds       : angle       5.24633 (  746)
  covalent geometry    : bond        0.00448 ( 6722)
  covalent geometry    : angle       0.64204 ( 9293)

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 75
  time to evaluate  : 0.684 
Fit side-chains
REVERT: B  298 ARG cc_start: 0.6670 (ttp-110) cc_final: 0.6345 (mtp180)
REVERT: B  307 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.8070 (tttp)
REVERT: B  330 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7035 (tp30)
REVERT: B  457 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7840 (ttmt)
REVERT: A  367 SER cc_start: 0.7937 (m) cc_final: 0.7269 (p)
REVERT: A  484 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8080 (tp)
  outliers start: 29
  outliers final: 18
  residues processed: 96
  average time/residue: 1.2804
  time to fit residues: 129.1192
Evaluate side-chains
  96 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 74
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  127 ASP
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  307 LYS
Chi-restraints excluded: chain B residue  330 GLU
Chi-restraints excluded: chain B residue  341 TYR
Chi-restraints excluded: chain B residue  343 LEU
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  421 THR
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  457 LYS
Chi-restraints excluded: chain B residue  466 ILE
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain A residue  514 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 39 optimal weight:    0.4980
   chunk 54 optimal weight:    0.7980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** B  29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 281 GLN
A 409 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.168521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.138792 restraints weight = 5857.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.3693 rms_B_bonded: 1.44
r_work: 0.3588 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3480 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.1226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6722  Z= 0.190
  Angle     :  0.636   8.494   9293  Z= 0.332
  Chirality :  0.042   0.155   1047
  Planarity :  0.005   0.056   1043
  Dihedral  : 19.269 164.764   1326
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 12.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 28.45 %
    Favored  : 67.11 %
  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: -0.29 (0.32), residues: 698
  helix:  0.44 (0.34), residues: 218
  sheet: -0.57 (0.40), residues: 165
  loop : -0.27 (0.37), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 510 
 HIS   0.003   0.001   HIS B 166 
 PHE   0.023   0.002   PHE B 255 
 TYR   0.025   0.002   TYR B  84 
 ARG   0.013   0.001   ARG B 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05452 (  269)
  hydrogen bonds       : angle       5.20414 (  746)
  covalent geometry    : bond        0.00431 ( 6722)
  covalent geometry    : angle       0.63605 ( 9293)

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 75
  time to evaluate  : 0.682 
Fit side-chains
REVERT: B  110 LEU cc_start: 0.7692 (mp) cc_final: 0.7472 (mp)
REVERT: B  298 ARG cc_start: 0.6633 (ttp-110) cc_final: 0.6342 (mtp180)
REVERT: B  307 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.8066 (tttp)
REVERT: B  330 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7024 (tp30)
REVERT: B  457 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7827 (ttmt)
REVERT: A  367 SER cc_start: 0.7934 (m) cc_final: 0.7262 (p)
REVERT: A  484 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8078 (tp)
  outliers start: 27
  outliers final: 17
  residues processed: 96
  average time/residue: 1.2474
  time to fit residues: 125.9497
Evaluate side-chains
  94 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 73
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  127 ASP
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  307 LYS
Chi-restraints excluded: chain B residue  330 GLU
Chi-restraints excluded: chain B residue  341 TYR
Chi-restraints excluded: chain B residue  343 LEU
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  421 THR
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  457 LYS
Chi-restraints excluded: chain B residue  466 ILE
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain A residue  514 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   chunk 40 optimal weight:    0.6980
   chunk 13 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0170
   chunk 9 optimal weight:    0.4980
   chunk 57 optimal weight:    0.9980
   overall best weight:    0.5618

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

Flipped N/Q/H residues before XYZ refinement:
B   7 GLN
** B  29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 281 GLN
A 409 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.171132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.141842 restraints weight = 5838.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.3727 rms_B_bonded: 1.43
r_work: 0.3623 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3515 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.1277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6722  Z= 0.157
  Angle     :  0.610   8.681   9293  Z= 0.318
  Chirality :  0.041   0.156   1047
  Planarity :  0.005   0.059   1043
  Dihedral  : 19.236 164.506   1326
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 28.78 %
    Favored  : 67.11 %
  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: -0.19 (0.32), residues: 698
  helix:  0.58 (0.34), residues: 218
  sheet: -0.54 (0.39), residues: 169
  loop : -0.22 (0.37), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 198 
 HIS   0.003   0.001   HIS B 166 
 PHE   0.023   0.002   PHE B 255 
 TYR   0.023   0.002   TYR B  84 
 ARG   0.014   0.001   ARG B 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05321 (  269)
  hydrogen bonds       : angle       5.08498 (  746)
  covalent geometry    : bond        0.00357 ( 6722)
  covalent geometry    : angle       0.60978 ( 9293)

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 79
  time to evaluate  : 0.689 
Fit side-chains
REVERT: B  298 ARG cc_start: 0.6728 (ttp-110) cc_final: 0.6402 (mtp180)
REVERT: B  330 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6955 (tp30)
REVERT: B  457 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7779 (ttmt)
REVERT: A  367 SER cc_start: 0.7917 (m) cc_final: 0.7255 (p)
REVERT: A  442 ARG cc_start: 0.6753 (mtt-85) cc_final: 0.6538 (mtt-85)
REVERT: A  484 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8035 (tp)
REVERT: A  508 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7158 (mm-30)
  outliers start: 25
  outliers final: 18
  residues processed: 97
  average time/residue: 1.1868
  time to fit residues: 121.4628
Evaluate side-chains
  97 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 76
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  127 ASP
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  330 GLU
Chi-restraints excluded: chain B residue  341 TYR
Chi-restraints excluded: chain B residue  343 LEU
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  421 THR
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  457 LYS
Chi-restraints excluded: chain B residue  466 ILE
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain A residue  514 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0980
   chunk 67 optimal weight:    5.9990
   chunk 58 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
** B  29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 281 GLN
A 409 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.166366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.136499 restraints weight = 5916.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.3668 rms_B_bonded: 1.45
r_work: 0.3563 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3455 rms_B_bonded: 3.13 restraints_weight: 0.2500
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.1318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   6722  Z= 0.248
  Angle     :  0.689   8.359   9293  Z= 0.357
  Chirality :  0.045   0.202   1047
  Planarity :  0.005   0.050   1043
  Dihedral  : 19.305 165.462   1326
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 12.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 29.28 %
    Favored  : 66.94 %
  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: -0.39 (0.32), residues: 698
  helix:  0.32 (0.33), residues: 217
  sheet: -0.63 (0.40), residues: 165
  loop : -0.29 (0.36), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 510 
 HIS   0.004   0.001   HIS B 166 
 PHE   0.020   0.002   PHE B 255 
 TYR   0.028   0.002   TYR B  84 
 ARG   0.014   0.001   ARG B 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05748 (  269)
  hydrogen bonds       : angle       5.28177 (  746)
  covalent geometry    : bond        0.00564 ( 6722)
  covalent geometry    : angle       0.68858 ( 9293)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7558.15 seconds
wall clock time: 135 minutes 33.47 seconds (8133.47 seconds total)