Starting phenix.real_space_refine
on Fri Aug 22 15:04:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8el7_28223/08_2025/8el7_28223.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8el7_28223/08_2025/8el7_28223.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8el7_28223/08_2025/8el7_28223.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8el7_28223/08_2025/8el7_28223.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8el7_28223/08_2025/8el7_28223.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8el7_28223/08_2025/8el7_28223.map"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.198
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: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      27      5.16       5
     C    2921      2.51       5
     N     802      2.21       5
     O     810      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4562
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1134
      Number of conformers: 3
      Conformer: "A"
        Number of residues, atoms: 146, 1118
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 6, 'TRANS': 139}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 107
          Unresolved non-hydrogen angles: 134
          Unresolved non-hydrogen dihedrals: 91
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 6, 'HIS:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 7, 'TRP:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 87
      Conformer: "B"
        Number of residues, atoms: 146, 1118
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 6, 'TRANS': 139}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 107
          Unresolved non-hydrogen angles: 134
          Unresolved non-hydrogen dihedrals: 91
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 6, 'HIS:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 7, 'TRP:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 87
          bond proxies already assigned to first conformer: 1130
      Conformer: "C"
        Number of residues, atoms: 146, 1118
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 6, 'TRANS': 139}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 107
          Unresolved non-hydrogen angles: 134
          Unresolved non-hydrogen dihedrals: 91
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 6, 'HIS:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 7, 'TRP:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 87
          bond proxies already assigned to first conformer: 1130
    Chain: "B"
      Number of atoms: 3423
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 458, 3423
          Classifications: {'peptide': 458}
          Incomplete info: {'truncation_to_alanine': 59}
          Link IDs: {'PTRANS': 15, 'TRANS': 442}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 230
          Unresolved non-hydrogen angles: 282
          Unresolved non-hydrogen dihedrals: 188
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 19, 'ARG:plan': 4, 'TYR:plan': 1, 'ASP:plan': 15, 'GLN:plan1': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'TPO:plan-1': 1}
          Unresolved non-hydrogen planarities: 171
    Chain: "B"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Classifications: {'water': 5}
          Link IDs: {None: 4}
  Time building chain proxies: 1.78, per 1000 atoms: 0.39
  Number of scatterers: 4562
  At special positions: 0
  Unit cell: (54.5344, 80.0974, 110.773, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      27     16.00
     P       2     15.00
     O     810      8.00
     N     802      7.00
     C    2921      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.41
  Conformation dependent library (CDL) restraints added in 256.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1168

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 1 sheets defined
      67.2% alpha, 3.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 251 through 264
      removed outlier: 3.652A  pdb=" N   ALA A 255 " --> pdb=" O   ARG A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 269
      removed outlier: 3.517A  pdb=" N   LEU A 268 " --> pdb=" O   ASN A 265 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ARG A 269 " --> pdb=" O   ARG A 266 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 265 through 269'
    Processing helix  chain 'A' and resid 279 through 290
      removed outlier: 3.762A  pdb=" N   GLY A 290 " --> pdb=" O   LYS A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 297
    Processing helix  chain 'A' and resid 298 through 304
    Processing helix  chain 'A' and resid 317 through 337
      removed outlier: 3.720A  pdb=" N   THR A 321 " --> pdb=" O   ASP A 317 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   PHE A 331 " --> pdb=" O   ILE A 327 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   ILE A 334 " --> pdb=" O   GLU A 330 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   SER A 335 " --> pdb=" O   PHE A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 376
    Processing helix  chain 'B' and resid 4 through 11
    Processing helix  chain 'B' and resid 14 through 29
      removed outlier: 4.129A  pdb=" N   ILE B  18 " --> pdb=" O   GLU B  14 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   GLU B  19 " --> pdb=" O   ALA B  15 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 38
      No H-bonds generated for 'chain 'B' and resid 36 through 38'
    Processing helix  chain 'B' and resid 39 through 56
      removed outlier: 3.512A  pdb=" N   PHE B  51 " --> pdb=" O   CYS B  47 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   VAL B  55 " --> pdb=" O   PHE B  51 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   LYS B  56 " --> pdb=" O   LYS B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 74
    Processing helix  chain 'B' and resid 85 through 96
      removed outlier: 3.678A  pdb=" N   MET B  89 " --> pdb=" O   THR B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 128
    Processing helix  chain 'B' and resid 129 through 138
      removed outlier: 3.597A  pdb=" N   GLN B 133 " --> pdb=" O   GLN B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 151
      removed outlier: 3.837A  pdb=" N   LYS B 143 " --> pdb=" O   ASN B 139 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 157 through 175
    Processing helix  chain 'B' and resid 176 through 184
    Processing helix  chain 'B' and resid 187 through 201
      removed outlier: 4.103A  pdb=" N   LEU B 191 " --> pdb=" O   GLN B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 220 through 238
      removed outlier: 3.535A  pdb=" N   ASN B 236 " --> pdb=" O   LYS B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 246 through 248
      No H-bonds generated for 'chain 'B' and resid 246 through 248'
    Processing helix  chain 'B' and resid 249 through 264
    Processing helix  chain 'B' and resid 270 through 286
    Processing helix  chain 'B' and resid 287 through 288
      No H-bonds generated for 'chain 'B' and resid 287 through 288'
    Processing helix  chain 'B' and resid 289 through 297
      removed outlier: 4.747A  pdb=" N   ASP B 294 " --> pdb=" O   SER B 291 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   VAL B 295 " --> pdb=" O   CYS B 292 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   LEU B 296 " --> pdb=" O   LEU B 293 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ILE B 297 " --> pdb=" O   ASP B 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 355
      removed outlier: 3.691A  pdb=" N   HIS B 343 " --> pdb=" O   MET B 339 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   LYS B 355 " --> pdb=" O   LYS B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 359 through 377
      removed outlier: 4.050A  pdb=" N   THR B 364 " --> pdb=" O   ARG B 360 " (cutoff:3.500A)
      Proline residue:  B 365  - end of helix
      removed outlier: 3.579A  pdb=" N   ALA B 376 " --> pdb=" O   GLU B 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 377 through 389
      removed outlier: 3.787A  pdb=" N   ARG B 381 " --> pdb=" O   HIS B 377 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ASP B 386 " --> pdb=" O   LYS B 382 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   GLN B 387 " --> pdb=" O   PHE B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 412
    Processing helix  chain 'B' and resid 413 through 415
      No H-bonds generated for 'chain 'B' and resid 413 through 415'
    Processing helix  chain 'B' and resid 417 through 432
      removed outlier: 3.618A  pdb=" N   LYS B 421 " --> pdb=" O   ASP B 417 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LEU B 428 " --> pdb=" O   ALA B 424 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 435 through 443
      removed outlier: 3.639A  pdb=" N   TYR B 442 " --> pdb=" O   SER B 438 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 456
    Processing helix  chain 'B' and resid 475 through 482
    Processing helix  chain 'B' and resid 483 through 485
      No H-bonds generated for 'chain 'B' and resid 483 through 485'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 209
      removed outlier: 6.217A  pdb=" N   ILE A 230 " --> pdb=" O   ILE A 274 " (cutoff:3.500A)
      removed outlier: 7.554A  pdb=" N   PHE A 276 " --> pdb=" O   ILE A 230 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   PHE A 232 " --> pdb=" O   PHE A 276 " (cutoff:3.500A)
      removed outlier: 7.575A  pdb=" N   ASN A 278 " --> pdb=" O   PHE A 232 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   VAL A 234 " --> pdb=" O   ASN A 278 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   VAL A 273 " --> pdb=" O   TYR A 346 " (cutoff:3.500A)
      removed outlier: 7.921A  pdb=" N   HIS A 348 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   LEU A 275 " --> pdb=" O   HIS A 348 " (cutoff:3.500A)

    245 hydrogen bonds defined for protein.
    710 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.65

  Time building geometry restraints manager: 0.54 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 728
        1.31 -     1.44: 1153
        1.44 -     1.56: 2711
        1.56 -     1.68: 2
        1.68 -     1.81: 38
  Bond restraints: 4632
  Sorted by residual:
  bond pdb=" O3P SEP B 468 "
       pdb=" P   SEP B 468 "
    ideal  model  delta    sigma   weight residual
    1.610  1.477  0.133 2.00e-02 2.50e+03 4.44e+01
  bond pdb=" C   ARG A 375 "
       pdb=" CA BARG A 375 "
    ideal  model  delta    sigma   weight residual
    1.522  1.430  0.091 1.40e-02 5.10e+03 4.26e+01
  bond pdb=" C   ARG A 375 "
       pdb=" CA CARG A 375 "
    ideal  model  delta    sigma   weight residual
    1.522  1.430  0.091 1.40e-02 5.10e+03 4.26e+01
  bond pdb=" O1P SEP B 468 "
       pdb=" P   SEP B 468 "
    ideal  model  delta    sigma   weight residual
    1.610  1.480  0.130 2.00e-02 2.50e+03 4.22e+01
  bond pdb=" O2P SEP B 468 "
       pdb=" P   SEP B 468 "
    ideal  model  delta    sigma   weight residual
    1.610  1.481  0.129 2.00e-02 2.50e+03 4.16e+01
  ... (remaining 4627 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.52: 6104
        1.52 -     3.03: 145
        3.03 -     4.55: 33
        4.55 -     6.06: 10
        6.06 -     7.58: 3
  Bond angle restraints: 6295
  Sorted by residual:
  angle pdb=" N   GLU B   4 "
        pdb=" CA  GLU B   4 "
        pdb=" C   GLU B   4 "
      ideal   model   delta    sigma   weight residual
     111.28  115.77   -4.49 1.09e+00 8.42e-01 1.70e+01
  angle pdb=" C   TRP B 466 "
        pdb=" N   TYR B 467 "
        pdb=" CA  TYR B 467 "
      ideal   model   delta    sigma   weight residual
     121.70  114.71    6.99 1.80e+00 3.09e-01 1.51e+01
  angle pdb=" CA  TRP B 466 "
        pdb=" C   TRP B 466 "
        pdb=" N   TYR B 467 "
      ideal   model   delta    sigma   weight residual
     116.02  121.32   -5.30 1.42e+00 4.96e-01 1.39e+01
  angle pdb=" N   ALA B  15 "
        pdb=" CA  ALA B  15 "
        pdb=" C   ALA B  15 "
      ideal   model   delta    sigma   weight residual
     113.38  117.91   -4.53 1.23e+00 6.61e-01 1.35e+01
  angle pdb=" N   GLY B  13 "
        pdb=" CA  GLY B  13 "
        pdb=" C   GLY B  13 "
      ideal   model   delta    sigma   weight residual
     112.73  116.85   -4.12 1.20e+00 6.94e-01 1.18e+01
  ... (remaining 6290 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.32: 2582
       17.32 -    34.64: 188
       34.64 -    51.96: 31
       51.96 -    69.28: 6
       69.28 -    86.60: 5
  Dihedral angle restraints: 2812
    sinusoidal: 1029
      harmonic: 1783
  Sorted by residual:
  dihedral pdb=" CA  GLY B  13 "
           pdb=" C   GLY B  13 "
           pdb=" N   GLU B  14 "
           pdb=" CA  GLU B  14 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.43  -24.57     0      5.00e+00 4.00e-02 2.42e+01
  dihedral pdb=" C   TPO B 473 "
           pdb=" N   TPO B 473 "
           pdb=" CA  TPO B 473 "
           pdb=" CB  TPO B 473 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.38   -9.22     0      2.50e+00 1.60e-01 1.36e+01
  dihedral pdb=" N   TRP B 466 "
           pdb=" C   TRP B 466 "
           pdb=" CA  TRP B 466 "
           pdb=" CB  TRP B 466 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  114.49    8.31     0      2.50e+00 1.60e-01 1.10e+01
  ... (remaining 2809 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 541
       0.038 -    0.077: 177
       0.077 -    0.115: 39
       0.115 -    0.154: 10
       0.154 -    0.192: 4
  Chirality restraints: 771
  Sorted by residual:
  chirality pdb=" CA  ALA B  15 "
            pdb=" N   ALA B  15 "
            pdb=" C   ALA B  15 "
            pdb=" CB  ALA B  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.29    0.19 2.00e-01 2.50e+01 9.25e-01
  chirality pdb=" CA BARG A 375 "
            pdb=" N   ARG A 375 "
            pdb=" C   ARG A 375 "
            pdb=" CB BARG A 375 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.05e-01
  chirality pdb=" CA CARG A 375 "
            pdb=" N   ARG A 375 "
            pdb=" C   ARG A 375 "
            pdb=" CB CARG A 375 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.05e-01
  ... (remaining 768 not shown)

  Planarity restraints: 789
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 463 "    0.014 2.00e-02 2.50e+03   2.81e-02 7.92e+00
        pdb=" C   GLY B 463 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   GLY B 463 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ASP B 464 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B   5 "    0.007 2.00e-02 2.50e+03   1.37e-02 1.88e+00
        pdb=" C   ARG B   5 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   ARG B   5 "    0.009 2.00e-02 2.50e+03
        pdb=" N   ALA B   6 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 478 "   -0.006 2.00e-02 2.50e+03   1.18e-02 1.40e+00
        pdb=" C   TYR B 478 "    0.020 2.00e-02 2.50e+03
        pdb=" O   TYR B 478 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   LYS B 479 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 786 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.82: 1226
        2.82 -     3.34: 4034
        3.34 -     3.86: 6742
        3.86 -     4.38: 7705
        4.38 -     4.90: 14105
  Nonbonded interactions: 33812
  Sorted by model distance:
  nonbonded pdb=" O   LEU B  80 "
            pdb=" OG1 THR B  84 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" O   LEU B  70 "
            pdb=" OG  SER B  74 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" N   GLU B   3 "
            pdb=" OE1 GLU B   3 "
     model   vdw
     2.356 3.120
  nonbonded pdb=" O   PRO B 399 "
            pdb=" ND2 ASN B 407 "
     model   vdw
     2.374 3.120
  nonbonded pdb=" N   ASP B 464 "
            pdb=" OD1 ASP B 464 "
     model   vdw
     2.407 3.120
  ... (remaining 33807 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=0.25 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:             0.960
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.970
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
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   0.133   4632  Z= 0.358
  Angle     :  0.611   7.578   6295  Z= 0.356
  Chirality :  0.042   0.192    771
  Planarity :  0.004   0.028    789
  Dihedral  : 13.128  86.604   1644
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 2.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.35), residues: 582
  helix:  1.64 (0.28), residues: 355
  sheet:  0.82 (0.97), residues: 32
  loop : -1.30 (0.42), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 328 
 TYR   0.009   0.001   TYR B 334 
 PHE   0.012   0.001   PHE B 163 
 TRP   0.011   0.001   TRP B 466 
 HIS   0.003   0.001   HIS B 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00585 ( 4632)
  covalent geometry    : angle       0.61097 ( 6295)
  hydrogen bonds       : bond        0.17679 (  245)
  hydrogen bonds       : angle       4.23490 (  710)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.180 
Fit side-chains
REVERT: B  181 GLN cc_start: 0.7585 (mt0) cc_final: 0.7336 (mt0)
REVERT: B  335 ASN cc_start: 0.7658 (t0) cc_final: 0.7363 (t0)
REVERT: B  372 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6962 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.7599
  time to fit residues: 45.4341
Evaluate side-chains
  46 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0370
   chunk 48 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9980
   chunk 26 optimal weight:    6.9990
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    0.9460

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

Flipped N/Q/H residues before XYZ refinement:
A 250 ASN
B 491 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.138168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.102549 restraints weight = 14514.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 3.33
r_work: 0.2973 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2926
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2926 r_free = 0.2926    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2925 r_free = 0.2925    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2925
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.1041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   4632  Z= 0.114
  Angle     :  0.482   5.786   6295  Z= 0.248
  Chirality :  0.039   0.133    771
  Planarity :  0.004   0.037    789
  Dihedral  :  3.479  12.763    653
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 1.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  6.29 %
    Favored  : 92.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.18 (0.36), residues: 582
  helix:  1.77 (0.28), residues: 368
  sheet:  0.70 (0.96), residues: 32
  loop : -1.30 (0.43), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 261 
 TYR   0.006   0.001   TYR A 344 
 PHE   0.014   0.001   PHE B 163 
 TRP   0.008   0.001   TRP B 466 
 HIS   0.005   0.001   HIS A 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 4632)
  covalent geometry    : angle       0.48160 ( 6295)
  hydrogen bonds       : bond        0.04844 (  245)
  hydrogen bonds       : angle       3.16948 (  710)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.220 
Fit side-chains
REVERT: B  335 ASN cc_start: 0.7836 (t0) cc_final: 0.7477 (t0)
REVERT: B  372 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7172 (mp0)
  outliers start: 6
  outliers final: 2
  residues processed: 45
  average time/residue: 0.7689
  time to fit residues: 35.7577
Evaluate side-chains
  43 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 41
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  405 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 0 optimal weight:    9.9990
   chunk 42 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   chunk 30 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 40 optimal weight:    0.2980
   chunk 13 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   overall best weight:    1.6186

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

Flipped N/Q/H residues before XYZ refinement:
** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 491 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.135215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.098484 restraints weight = 20596.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.3082 rms_B_bonded: 3.93
r_work: 0.2927 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.2927
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2932
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2932 r_free = 0.2932    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2932 r_free = 0.2932    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2932
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.1236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4632  Z= 0.146
  Angle     :  0.521   5.033   6295  Z= 0.268
  Chirality :  0.040   0.133    771
  Planarity :  0.004   0.038    789
  Dihedral  :  3.590  12.691    653
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 1.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  :  6.94 %
    Favored  : 91.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.27 (0.35), residues: 582
  helix:  1.86 (0.28), residues: 358
  sheet:  0.69 (0.95), residues: 32
  loop : -1.11 (0.42), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 366 
 TYR   0.008   0.001   TYR B 334 
 PHE   0.018   0.002   PHE B 163 
 TRP   0.006   0.001   TRP A 263 
 HIS   0.008   0.002   HIS A 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 4632)
  covalent geometry    : angle       0.52143 ( 6295)
  hydrogen bonds       : bond        0.06280 (  245)
  hydrogen bonds       : angle       3.32846 (  710)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 41
  time to evaluate  : 0.180 
Fit side-chains
REVERT: A  333 ARG cc_start: 0.6656 (OUTLIER) cc_final: 0.4805 (ptp90)
REVERT: B  335 ASN cc_start: 0.7857 (t0) cc_final: 0.7439 (t0)
REVERT: B  372 GLU cc_start: 0.7443 (mm-30) cc_final: 0.6882 (mp0)
  outliers start: 9
  outliers final: 4
  residues processed: 46
  average time/residue: 0.9151
  time to fit residues: 43.2596
Evaluate side-chains
  44 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  333 ARG
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  405 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 36 optimal weight:    6.9990
   chunk 11 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   chunk 49 optimal weight:    4.9990
   chunk 18 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 491 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.134010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.098602 restraints weight = 12689.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.3077 rms_B_bonded: 3.13
r_work: 0.2942 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2881
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2881 r_free = 0.2881    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2881 r_free = 0.2881    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2881
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.1371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   4632  Z= 0.167
  Angle     :  0.553   5.333   6295  Z= 0.282
  Chirality :  0.041   0.134    771
  Planarity :  0.004   0.038    789
  Dihedral  :  3.700  12.814    653
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 1.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  :  8.89 %
    Favored  : 88.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.12 (0.35), residues: 582
  helix:  1.75 (0.28), residues: 358
  sheet:  0.59 (0.94), residues: 32
  loop : -1.19 (0.42), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 366 
 TYR   0.009   0.002   TYR B 334 
 PHE   0.019   0.002   PHE B 163 
 TRP   0.006   0.001   TRP A 263 
 HIS   0.010   0.002   HIS B 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 4632)
  covalent geometry    : angle       0.55252 ( 6295)
  hydrogen bonds       : bond        0.06810 (  245)
  hydrogen bonds       : angle       3.42153 (  710)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 41
  time to evaluate  : 0.187 
Fit side-chains
REVERT: A  333 ARG cc_start: 0.6718 (OUTLIER) cc_final: 0.4823 (ptp90)
REVERT: B  150 LYS cc_start: 0.7103 (mtpp) cc_final: 0.6895 (mtmm)
REVERT: B  335 ASN cc_start: 0.7931 (t0) cc_final: 0.7484 (t0)
REVERT: B  372 GLU cc_start: 0.7450 (mm-30) cc_final: 0.6843 (mp0)
  outliers start: 10
  outliers final: 7
  residues processed: 47
  average time/residue: 0.8479
  time to fit residues: 40.9901
Evaluate side-chains
  48 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  333 ARG
Chi-restraints excluded: chain B residue   10 VAL
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  405 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 36 optimal weight:    4.9990
   chunk 48 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 57 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 14 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   chunk 3 optimal weight:    0.8980
   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 491 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.136184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.099735 restraints weight = 20235.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.3019 rms_B_bonded: 3.76
r_work: 0.2852 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2936
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2936 r_free = 0.2936    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2936 r_free = 0.2936    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2936
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.1354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4632  Z= 0.139
  Angle     :  0.502   5.038   6295  Z= 0.258
  Chirality :  0.040   0.132    771
  Planarity :  0.004   0.037    789
  Dihedral  :  3.613  15.994    653
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 1.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  :  9.54 %
    Favored  : 88.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.25 (0.35), residues: 582
  helix:  1.87 (0.28), residues: 359
  sheet:  0.68 (0.94), residues: 32
  loop : -1.21 (0.43), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 366 
 TYR   0.008   0.001   TYR B 334 
 PHE   0.017   0.002   PHE B 163 
 TRP   0.004   0.001   TRP A 263 
 HIS   0.010   0.002   HIS B 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 4632)
  covalent geometry    : angle       0.50185 ( 6295)
  hydrogen bonds       : bond        0.05852 (  245)
  hydrogen bonds       : angle       3.31039 (  710)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 41
  time to evaluate  : 0.184 
Fit side-chains
REVERT: A  333 ARG cc_start: 0.6627 (OUTLIER) cc_final: 0.4799 (ptp90)
REVERT: B  150 LYS cc_start: 0.6962 (mtpp) cc_final: 0.6634 (mtmm)
REVERT: B  335 ASN cc_start: 0.7923 (t0) cc_final: 0.7463 (t0)
REVERT: B  372 GLU cc_start: 0.7400 (mm-30) cc_final: 0.6860 (mp0)
  outliers start: 10
  outliers final: 8
  residues processed: 47
  average time/residue: 0.8528
  time to fit residues: 41.2250
Evaluate side-chains
  48 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 39
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  333 ARG
Chi-restraints excluded: chain B residue   10 VAL
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  405 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   chunk 38 optimal weight:    8.9990
   chunk 32 optimal weight:    0.8980
   chunk 16 optimal weight:    5.9990
   chunk 44 optimal weight:    0.8980
   chunk 37 optimal weight:    0.7980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
B 491 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.136812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.101688 restraints weight = 13679.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3053 rms_B_bonded: 3.17
r_work: 0.2898 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2976
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2976 r_free = 0.2976    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2976 r_free = 0.2976    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2976
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.1366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4632  Z= 0.127
  Angle     :  0.481   5.023   6295  Z= 0.248
  Chirality :  0.039   0.133    771
  Planarity :  0.004   0.037    789
  Dihedral  :  3.558  18.332    653
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 1.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  :  9.76 %
    Favored  : 88.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.34 (0.35), residues: 582
  helix:  1.96 (0.28), residues: 359
  sheet:  0.67 (0.95), residues: 32
  loop : -1.19 (0.43), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 366 
 TYR   0.008   0.001   TYR B 334 
 PHE   0.016   0.001   PHE B 163 
 TRP   0.004   0.001   TRP A 263 
 HIS   0.009   0.001   HIS B 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 4632)
  covalent geometry    : angle       0.48058 ( 6295)
  hydrogen bonds       : bond        0.05416 (  245)
  hydrogen bonds       : angle       3.24617 (  710)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 41
  time to evaluate  : 0.186 
Fit side-chains
REVERT: A  333 ARG cc_start: 0.6585 (OUTLIER) cc_final: 0.4726 (ptp90)
REVERT: B  150 LYS cc_start: 0.6966 (mtpp) cc_final: 0.6632 (mtmm)
REVERT: B  335 ASN cc_start: 0.7908 (t0) cc_final: 0.7459 (t0)
REVERT: B  372 GLU cc_start: 0.7377 (mm-30) cc_final: 0.6838 (mp0)
  outliers start: 10
  outliers final: 8
  residues processed: 47
  average time/residue: 0.9112
  time to fit residues: 44.0188
Evaluate side-chains
  48 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 39
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  333 ARG
Chi-restraints excluded: chain B residue   10 VAL
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  405 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 19 optimal weight:    0.2980
   chunk 30 optimal weight:    4.9990
   chunk 54 optimal weight:    4.9990
   chunk 38 optimal weight:   10.0000
   chunk 2 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 491 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.135370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.099145 restraints weight = 18685.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.3018 rms_B_bonded: 3.64
r_work: 0.2850 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2843
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2843 r_free = 0.2843    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2843 r_free = 0.2843    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2843
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.1418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4632  Z= 0.145
  Angle     :  0.512   5.040   6295  Z= 0.263
  Chirality :  0.040   0.132    771
  Planarity :  0.004   0.037    789
  Dihedral  :  3.650  20.478    653
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 1.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  :  9.76 %
    Favored  : 88.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.22 (0.35), residues: 582
  helix:  1.87 (0.28), residues: 359
  sheet:  0.63 (0.95), residues: 32
  loop : -1.26 (0.43), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 366 
 TYR   0.009   0.001   TYR B 334 
 PHE   0.018   0.002   PHE B 163 
 TRP   0.005   0.001   TRP A 263 
 HIS   0.010   0.002   HIS B 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 4632)
  covalent geometry    : angle       0.51167 ( 6295)
  hydrogen bonds       : bond        0.06102 (  245)
  hydrogen bonds       : angle       3.32633 (  710)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 39
  time to evaluate  : 0.199 
Fit side-chains
REVERT: A  333 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.4885 (ptp90)
REVERT: B  150 LYS cc_start: 0.7067 (mtpp) cc_final: 0.6754 (mtmm)
REVERT: B  335 ASN cc_start: 0.7979 (t0) cc_final: 0.7520 (t0)
REVERT: B  372 GLU cc_start: 0.7534 (mm-30) cc_final: 0.6952 (mp0)
  outliers start: 10
  outliers final: 8
  residues processed: 45
  average time/residue: 0.9217
  time to fit residues: 42.6746
Evaluate side-chains
  48 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 39
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  333 ARG
Chi-restraints excluded: chain B residue   10 VAL
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  405 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 34 optimal weight:    7.9990
   chunk 7 optimal weight:    0.8980
   chunk 23 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 491 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.134405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.099566 restraints weight = 13690.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.3021 rms_B_bonded: 3.14
r_work: 0.2864 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2869
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2869 r_free = 0.2869    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2869 r_free = 0.2869    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2869
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.1480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   4632  Z= 0.166
  Angle     :  0.541   5.319   6295  Z= 0.278
  Chirality :  0.041   0.133    771
  Planarity :  0.004   0.037    789
  Dihedral  :  3.779  23.052    653
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 1.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  :  9.54 %
    Favored  : 88.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.10 (0.35), residues: 582
  helix:  1.79 (0.28), residues: 358
  sheet:  0.55 (0.95), residues: 32
  loop : -1.34 (0.42), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 319 
 TYR   0.010   0.002   TYR B 334 
 PHE   0.019   0.002   PHE B 163 
 TRP   0.005   0.001   TRP A 263 
 HIS   0.010   0.002   HIS B 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 4632)
  covalent geometry    : angle       0.54150 ( 6295)
  hydrogen bonds       : bond        0.06740 (  245)
  hydrogen bonds       : angle       3.42277 (  710)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.185 
Fit side-chains
REVERT: A  333 ARG cc_start: 0.6672 (OUTLIER) cc_final: 0.4816 (ptp90)
REVERT: B  335 ASN cc_start: 0.7979 (t0) cc_final: 0.7521 (t0)
REVERT: B  372 GLU cc_start: 0.7451 (mm-30) cc_final: 0.6777 (mp0)
  outliers start: 11
  outliers final: 9
  residues processed: 49
  average time/residue: 0.8426
  time to fit residues: 42.4701
Evaluate side-chains
  50 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 40
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  333 ARG
Chi-restraints excluded: chain B residue   10 VAL
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  487 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 25 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   chunk 34 optimal weight:    7.9990
   chunk 8 optimal weight:    0.6980
   chunk 46 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0670
   chunk 38 optimal weight:    8.9990
   chunk 14 optimal weight:    6.9990
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.6718

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

Flipped N/Q/H residues before XYZ refinement:
B 491 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.139599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.108045 restraints weight = 18711.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 4.46
r_work: 0.3047 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3024
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3024
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.1413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   4632  Z= 0.094
  Angle     :  0.424   4.997   6295  Z= 0.221
  Chirality :  0.037   0.128    771
  Planarity :  0.003   0.035    789
  Dihedral  :  3.448  26.690    653
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 1.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 10.20 %
    Favored  : 87.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.57 (0.36), residues: 582
  helix:  2.21 (0.28), residues: 358
  sheet:  0.72 (0.96), residues: 32
  loop : -1.26 (0.43), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 322 
 TYR   0.006   0.001   TYR B 334 
 PHE   0.014   0.001   PHE A 232 
 TRP   0.002   0.000   TRP B 466 
 HIS   0.010   0.001   HIS B 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00192 ( 4632)
  covalent geometry    : angle       0.42446 ( 6295)
  hydrogen bonds       : bond        0.03808 (  245)
  hydrogen bonds       : angle       3.10601 (  710)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 42
  time to evaluate  : 0.193 
Fit side-chains
REVERT: A  333 ARG cc_start: 0.6506 (OUTLIER) cc_final: 0.4683 (ptp90)
REVERT: B  335 ASN cc_start: 0.7851 (t0) cc_final: 0.7432 (t0)
REVERT: B  372 GLU cc_start: 0.7358 (mm-30) cc_final: 0.6687 (mp0)
  outliers start: 9
  outliers final: 6
  residues processed: 47
  average time/residue: 0.8499
  time to fit residues: 41.1482
Evaluate side-chains
  47 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 40
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  333 ARG
Chi-restraints excluded: chain B residue   10 VAL
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  405 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 12 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   chunk 34 optimal weight:    7.9990
   chunk 35 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9990
   chunk 6 optimal weight:    3.9990
   chunk 57 optimal weight:    5.9990
   chunk 20 optimal weight:    0.8980
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 491 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.133315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.096477 restraints weight = 24299.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.2994 rms_B_bonded: 4.06
r_work: 0.2818 rms_B_bonded: 4.38 restraints_weight: 0.5000
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2913
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2913 r_free = 0.2913    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2913 r_free = 0.2913    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2913
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.1489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   4632  Z= 0.164
  Angle     :  0.534   5.434   6295  Z= 0.273
  Chirality :  0.041   0.131    771
  Planarity :  0.004   0.036    789
  Dihedral  :  3.673  24.754    653
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 1.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 10.85 %
    Favored  : 87.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.27 (0.35), residues: 582
  helix:  1.94 (0.28), residues: 358
  sheet:  0.61 (0.96), residues: 32
  loop : -1.29 (0.42), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 319 
 TYR   0.009   0.002   TYR B 334 
 PHE   0.019   0.002   PHE B 163 
 TRP   0.006   0.001   TRP A 263 
 HIS   0.010   0.002   HIS B 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 4632)
  covalent geometry    : angle       0.53422 ( 6295)
  hydrogen bonds       : bond        0.06533 (  245)
  hydrogen bonds       : angle       3.35186 (  710)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 40
  time to evaluate  : 0.230 
Fit side-chains
REVERT: A  333 ARG cc_start: 0.6610 (OUTLIER) cc_final: 0.4763 (ptp90)
REVERT: B  335 ASN cc_start: 0.7942 (t0) cc_final: 0.7481 (t0)
REVERT: B  372 GLU cc_start: 0.7467 (mm-30) cc_final: 0.6871 (mp0)
  outliers start: 9
  outliers final: 6
  residues processed: 44
  average time/residue: 0.8968
  time to fit residues: 40.6295
Evaluate side-chains
  46 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 39
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  333 ARG
Chi-restraints excluded: chain B residue   10 VAL
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  405 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 32 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   chunk 43 optimal weight:    0.0470
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.7078

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

Flipped N/Q/H residues before XYZ refinement:
B 491 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.139348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.102422 restraints weight = 18980.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.3060 rms_B_bonded: 3.86
r_work: 0.2893 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2882
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2882 r_free = 0.2882    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2882 r_free = 0.2882    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2882
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.1420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   4632  Z= 0.099
  Angle     :  0.434   4.970   6295  Z= 0.226
  Chirality :  0.038   0.128    771
  Planarity :  0.003   0.036    789
  Dihedral  :  3.489  26.420    653
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 1.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 11.06 %
    Favored  : 86.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.62 (0.36), residues: 582
  helix:  2.24 (0.28), residues: 356
  sheet:  0.81 (0.97), residues: 32
  loop : -1.19 (0.43), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 462 
 TYR   0.006   0.001   TYR B 334 
 PHE   0.017   0.001   PHE A 232 
 TRP   0.001   0.000   TRP B 466 
 HIS   0.009   0.001   HIS B 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00204 ( 4632)
  covalent geometry    : angle       0.43444 ( 6295)
  hydrogen bonds       : bond        0.04171 (  245)
  hydrogen bonds       : angle       3.14255 (  710)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1769.73 seconds
wall clock time: 31 minutes 3.36 seconds (1863.36 seconds total)