Starting phenix.real_space_refine
on Thu Mar 13 04:07:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tpn_41478/03_2025/8tpn_41478.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tpn_41478/03_2025/8tpn_41478.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.07
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tpn_41478/03_2025/8tpn_41478.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tpn_41478/03_2025/8tpn_41478.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tpn_41478/03_2025/8tpn_41478.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tpn_41478/03_2025/8tpn_41478.cif"
  }
  resolution = 4.07
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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
     Ca      4      9.91       5
     S      36      5.16       5
     C    5662      2.51       5
     N    1414      2.21       5
     O    1496      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8612
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4304
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 551, 4304
          Classifications: {'peptide': 551}
          Incomplete info: {'truncation_to_alanine': 35}
          Link IDs: {'PTRANS': 21, 'TRANS': 529}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 159
          Unresolved non-hydrogen angles: 196
          Unresolved non-hydrogen dihedrals: 137
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 9, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 114
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 8.36, per 1000 atoms: 0.97
  Number of scatterers: 8612
  At special positions: 0
  Unit cell: (111.93, 115.57, 96.46, 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)
     Ca      4     19.99
     S      36     16.00
     O    1496      8.00
     N    1414      7.00
     C    5662      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.61
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2096

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 2 sheets defined
      74.4% alpha, 2.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 50
      removed outlier: 3.511A  pdb=" N   VAL A  50 " --> pdb=" O   ALA A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 90
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 4.438A  pdb=" N   ASP A 107 " --> pdb=" O   GLN A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 125
    Processing helix  chain 'A' and resid 126 through 130
    Processing helix  chain 'A' and resid 152 through 164
    Processing helix  chain 'A' and resid 170 through 182
      removed outlier: 3.775A  pdb=" N   ILE A 174 " --> pdb=" O   GLU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 199
    Processing helix  chain 'A' and resid 199 through 212
    Processing helix  chain 'A' and resid 217 through 246
    Processing helix  chain 'A' and resid 250 through 254
    Processing helix  chain 'A' and resid 280 through 289
      removed outlier: 3.948A  pdb=" N   ARG A 284 " --> pdb=" O   PRO A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 317
      removed outlier: 3.640A  pdb=" N   PHE A 294 " --> pdb=" O   LEU A 290 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   LEU A 305 " --> pdb=" O   ALA A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 358
      Proline residue:  A 341  - end of helix
      removed outlier: 3.542A  pdb=" N   VAL A 346 " --> pdb=" O   THR A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 392
      removed outlier: 5.643A  pdb=" N   ALA A 385 " --> pdb=" O   THR A 381 " (cutoff:3.500A)
      removed outlier: 5.537A  pdb=" N   LEU A 386 " --> pdb=" O   SER A 382 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   VAL A 392 " --> pdb=" O   PHE A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 411
      removed outlier: 3.721A  pdb=" N   ALA A 411 " --> pdb=" O   TRP A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 431 through 449
      removed outlier: 3.607A  pdb=" N   TYR A 439 " --> pdb=" O   ASN A 435 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   ALA A 444 " --> pdb=" O   PHE A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 465
    Processing helix  chain 'A' and resid 482 through 494
      removed outlier: 3.873A  pdb=" N   THR A 494 " --> pdb=" O   ARG A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 500 through 518
      removed outlier: 3.614A  pdb=" N   SER A 518 " --> pdb=" O   VAL A 514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 523 through 545
      removed outlier: 3.856A  pdb=" N   CYS A 527 " --> pdb=" O   LEU A 523 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   VAL A 530 " --> pdb=" O   CYS A 526 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   ARG A 537 " --> pdb=" O   TRP A 533 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   ALA A 540 " --> pdb=" O   LEU A 536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 584
      removed outlier: 3.670A  pdb=" N   ALA A 564 " --> pdb=" O   PRO A 560 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   SER A 577 " --> pdb=" O   SER A 573 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ALA A 578 " --> pdb=" O   ILE A 574 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   SER A 584 " --> pdb=" O   VAL A 580 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 599 through 625
      removed outlier: 3.590A  pdb=" N   SER A 625 " --> pdb=" O   ARG A 621 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 711
    Processing helix  chain 'B' and resid 32 through 50
      removed outlier: 3.511A  pdb=" N   VAL B  50 " --> pdb=" O   ALA B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 90
    Processing helix  chain 'B' and resid 103 through 108
      removed outlier: 4.437A  pdb=" N   ASP B 107 " --> pdb=" O   GLN B 103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 125
    Processing helix  chain 'B' and resid 126 through 130
    Processing helix  chain 'B' and resid 152 through 164
    Processing helix  chain 'B' and resid 170 through 182
      removed outlier: 3.775A  pdb=" N   ILE B 174 " --> pdb=" O   GLU B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 199
    Processing helix  chain 'B' and resid 199 through 212
    Processing helix  chain 'B' and resid 217 through 246
    Processing helix  chain 'B' and resid 250 through 254
    Processing helix  chain 'B' and resid 280 through 289
      removed outlier: 3.948A  pdb=" N   ARG B 284 " --> pdb=" O   PRO B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 290 through 317
      removed outlier: 3.640A  pdb=" N   PHE B 294 " --> pdb=" O   LEU B 290 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   LEU B 305 " --> pdb=" O   ALA B 301 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 331 through 358
      Proline residue:  B 341  - end of helix
      removed outlier: 3.542A  pdb=" N   VAL B 346 " --> pdb=" O   THR B 342 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 362 through 392
      removed outlier: 5.644A  pdb=" N   ALA B 385 " --> pdb=" O   THR B 381 " (cutoff:3.500A)
      removed outlier: 5.537A  pdb=" N   LEU B 386 " --> pdb=" O   SER B 382 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   VAL B 392 " --> pdb=" O   PHE B 388 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 403 through 411
      removed outlier: 3.721A  pdb=" N   ALA B 411 " --> pdb=" O   TRP B 407 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 431 through 449
      removed outlier: 3.607A  pdb=" N   TYR B 439 " --> pdb=" O   ASN B 435 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   ALA B 444 " --> pdb=" O   PHE B 440 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 453 through 465
    Processing helix  chain 'B' and resid 482 through 494
      removed outlier: 3.872A  pdb=" N   THR B 494 " --> pdb=" O   ARG B 490 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 500 through 518
      removed outlier: 3.614A  pdb=" N   SER B 518 " --> pdb=" O   VAL B 514 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 523 through 545
      removed outlier: 3.855A  pdb=" N   CYS B 527 " --> pdb=" O   LEU B 523 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   VAL B 530 " --> pdb=" O   CYS B 526 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   ARG B 537 " --> pdb=" O   TRP B 533 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   ALA B 540 " --> pdb=" O   LEU B 536 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 560 through 584
      removed outlier: 3.670A  pdb=" N   ALA B 564 " --> pdb=" O   PRO B 560 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   SER B 577 " --> pdb=" O   SER B 573 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ALA B 578 " --> pdb=" O   ILE B 574 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   SER B 584 " --> pdb=" O   VAL B 580 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 599 through 625
      removed outlier: 3.590A  pdb=" N   SER B 625 " --> pdb=" O   ARG B 621 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 703 through 711
    Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 56
    Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 56

    598 hydrogen bonds defined for protein.
    1758 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: 2.49

  Time building geometry restraints manager: 2.95 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2670
        1.34 -     1.46: 2218
        1.46 -     1.58: 3886
        1.58 -     1.69: 0
        1.69 -     1.81: 58
  Bond restraints: 8832
  Sorted by residual:
  bond pdb=" C   VAL B 455 "
       pdb=" N   PRO B 456 "
    ideal  model  delta    sigma   weight residual
    1.335  1.346 -0.011 1.36e-02 5.41e+03 6.47e-01
  bond pdb=" C   ILE B 394 "
       pdb=" N   PRO B 395 "
    ideal  model  delta    sigma   weight residual
    1.335  1.345 -0.010 1.28e-02 6.10e+03 6.40e-01
  bond pdb=" C   VAL A 455 "
       pdb=" N   PRO A 456 "
    ideal  model  delta    sigma   weight residual
    1.335  1.346 -0.011 1.36e-02 5.41e+03 6.38e-01
  bond pdb=" C   PHE A 181 "
       pdb=" N   GLY A 182 "
    ideal  model  delta    sigma   weight residual
    1.335  1.329  0.006 7.50e-03 1.78e+04 6.36e-01
  bond pdb=" C   ILE A 394 "
       pdb=" N   PRO A 395 "
    ideal  model  delta    sigma   weight residual
    1.335  1.345 -0.010 1.28e-02 6.10e+03 6.05e-01
  ... (remaining 8827 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.37: 11797
        1.37 -     2.74: 181
        2.74 -     4.12: 32
        4.12 -     5.49: 14
        5.49 -     6.86: 4
  Bond angle restraints: 12028
  Sorted by residual:
  angle pdb=" N   GLY A 182 "
        pdb=" CA  GLY A 182 "
        pdb=" C   GLY A 182 "
      ideal   model   delta    sigma   weight residual
     111.21  114.35   -3.14 1.04e+00 9.25e-01 9.09e+00
  angle pdb=" N   GLY B 182 "
        pdb=" CA  GLY B 182 "
        pdb=" C   GLY B 182 "
      ideal   model   delta    sigma   weight residual
     111.21  114.31   -3.10 1.04e+00 9.25e-01 8.89e+00
  angle pdb=" CA  VAL A 455 "
        pdb=" C   VAL A 455 "
        pdb=" N   PRO A 456 "
      ideal   model   delta    sigma   weight residual
     118.88  122.02   -3.14 1.54e+00 4.22e-01 4.15e+00
  angle pdb=" CA  VAL B 455 "
        pdb=" C   VAL B 455 "
        pdb=" N   PRO B 456 "
      ideal   model   delta    sigma   weight residual
     118.88  121.99   -3.11 1.54e+00 4.22e-01 4.07e+00
  angle pdb=" C   PHE B 181 "
        pdb=" N   GLY B 182 "
        pdb=" CA  GLY B 182 "
      ideal   model   delta    sigma   weight residual
     122.63  120.64    1.99 1.03e+00 9.43e-01 3.73e+00
  ... (remaining 12023 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 4514
       17.92 -    35.85: 480
       35.85 -    53.77: 82
       53.77 -    71.69: 12
       71.69 -    89.62: 10
  Dihedral angle restraints: 5098
    sinusoidal: 1880
      harmonic: 3218
  Sorted by residual:
  dihedral pdb=" CA  THR A 441 "
           pdb=" C   THR A 441 "
           pdb=" N   VAL A 442 "
           pdb=" CA  VAL A 442 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.13  -16.87     0      5.00e+00 4.00e-02 1.14e+01
  dihedral pdb=" CA  THR B 441 "
           pdb=" C   THR B 441 "
           pdb=" N   VAL B 442 "
           pdb=" CA  VAL B 442 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.13  -16.87     0      5.00e+00 4.00e-02 1.14e+01
  dihedral pdb=" CB  GLU A 452 "
           pdb=" CG  GLU A 452 "
           pdb=" CD  GLU A 452 "
           pdb=" OE1 GLU A 452 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.62  -89.62     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 5095 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 928
       0.030 -    0.060: 289
       0.060 -    0.091: 116
       0.091 -    0.121: 35
       0.121 -    0.151: 6
  Chirality restraints: 1374
  Sorted by residual:
  chirality pdb=" CA  THR A 340 "
            pdb=" N   THR A 340 "
            pdb=" C   THR A 340 "
            pdb=" CB  THR A 340 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.38    0.15 2.00e-01 2.50e+01 5.69e-01
  chirality pdb=" CA  THR B 340 "
            pdb=" N   THR B 340 "
            pdb=" C   THR B 340 "
            pdb=" CB  THR B 340 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.38    0.15 2.00e-01 2.50e+01 5.64e-01
  chirality pdb=" CA  ILE A 147 "
            pdb=" N   ILE A 147 "
            pdb=" C   ILE A 147 "
            pdb=" CB  ILE A 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.90e-01
  ... (remaining 1371 not shown)

  Planarity restraints: 1496
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 292 "   -0.051 5.00e-02 4.00e+02   7.61e-02 9.27e+00
        pdb=" N   PRO A 293 "    0.132 5.00e-02 4.00e+02
        pdb=" CA  PRO A 293 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 293 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 292 "   -0.051 5.00e-02 4.00e+02   7.61e-02 9.26e+00
        pdb=" N   PRO B 293 "    0.132 5.00e-02 4.00e+02
        pdb=" CA  PRO B 293 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO B 293 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 439 "   -0.009 2.00e-02 2.50e+03   1.71e-02 2.91e+00
        pdb=" C   TYR A 439 "    0.029 2.00e-02 2.50e+03
        pdb=" O   TYR A 439 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   PHE A 440 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1493 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1291
        2.76 -     3.29: 8532
        3.29 -     3.83: 14341
        3.83 -     4.36: 13948
        4.36 -     4.90: 25865
  Nonbonded interactions: 63977
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 362 "
            pdb=" OD1 ASP B 364 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" OG1 THR A 362 "
            pdb=" OD1 ASP A 364 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" OH  TYR A  26 "
            pdb=" O   ALA A  36 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" OH  TYR B  26 "
            pdb=" O   ALA B  36 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" OH  TYR A 188 "
            pdb=" OD2 ASP A 539 "
     model   vdw
     2.235 3.040
  ... (remaining 63972 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     26.560
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
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      :  0.002   0.034   8832  Z= 0.150
  Angle     :  0.464   6.861  12028  Z= 0.249
  Chirality :  0.037   0.151   1374
  Planarity :  0.004   0.076   1496
  Dihedral  : 15.102  89.616   3002
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  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:  2.66 (0.26), residues: 1066
  helix:  2.61 (0.19), residues: 750
  sheet:  0.63 (0.91), residues: 48
  loop : -0.56 (0.37), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 163 
 HIS   0.002   0.000   HIS B 611 
 PHE   0.011   0.001   PHE A 187 
 TYR   0.009   0.001   TYR B 218 
 ARG   0.001   0.000   ARG B  45 

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.984 
Fit side-chains
REVERT: A  456 PRO cc_start: 0.8284 (Cg_exo) cc_final: 0.8061 (Cg_endo)
  outliers start: 0
  outliers final: 0
  residues processed: 116
  average time/residue: 0.1995
  time to fit residues: 33.9183
Evaluate side-chains
  87 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 1.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    0.5980
   chunk 83 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 86 optimal weight:    3.9990
   chunk 33 optimal weight:    0.6980
   chunk 52 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9980
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A  79 GLN
A 128 ASN
A 374 GLN
B  79 GLN
B 128 ASN
B 374 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.120951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.103209 restraints weight = 15213.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.101836 restraints weight = 15645.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.102618 restraints weight = 16838.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.0980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8832  Z= 0.214
  Angle     :  0.495   7.155  12028  Z= 0.267
  Chirality :  0.039   0.148   1374
  Planarity :  0.004   0.060   1496
  Dihedral  :  3.549  15.120   1166
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  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:  2.65 (0.26), residues: 1066
  helix:  2.55 (0.18), residues: 766
  sheet:  0.62 (0.91), residues: 48
  loop : -0.59 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 521 
 HIS   0.003   0.001   HIS A 127 
 PHE   0.010   0.001   PHE A 198 
 TYR   0.008   0.001   TYR B 220 
 ARG   0.003   0.000   ARG A 432 

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.920 
Fit side-chains
REVERT: A  286 LYS cc_start: 0.8314 (ttmt) cc_final: 0.7958 (tppt)
REVERT: A  456 PRO cc_start: 0.8404 (Cg_exo) cc_final: 0.8152 (Cg_endo)
REVERT: B  122 MET cc_start: 0.8517 (ttm) cc_final: 0.8300 (ttm)
REVERT: B  286 LYS cc_start: 0.8444 (ttmt) cc_final: 0.8168 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.1736
  time to fit residues: 29.8587
Evaluate side-chains
  89 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0980
   chunk 89 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0770
   chunk 79 optimal weight:    0.0670
   chunk 65 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   chunk 104 optimal weight:    0.0770
   chunk 106 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   overall best weight:    0.2634

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

Flipped N/Q/H residues before XYZ refinement:
A 374 GLN
B 445 GLN
B 531 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.131081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.112925 restraints weight = 14578.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.113685 restraints weight = 11117.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.114038 restraints weight = 9279.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.1184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8832  Z= 0.135
  Angle     :  0.455   6.898  12028  Z= 0.239
  Chirality :  0.037   0.163   1374
  Planarity :  0.004   0.053   1496
  Dihedral  :  3.465  16.309   1166
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  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:  2.78 (0.26), residues: 1066
  helix:  2.65 (0.18), residues: 766
  sheet:  0.59 (0.91), residues: 48
  loop : -0.56 (0.36), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 521 
 HIS   0.001   0.000   HIS B 143 
 PHE   0.011   0.001   PHE A  40 
 TYR   0.009   0.001   TYR A 613 
 ARG   0.006   0.000   ARG A 432 

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.879 
Fit side-chains
   revert: symmetry clash
REVERT: A  286 LYS cc_start: 0.8211 (ttmt) cc_final: 0.7902 (tppt)
REVERT: A  456 PRO cc_start: 0.8266 (Cg_exo) cc_final: 0.8009 (Cg_endo)
REVERT: B   41 VAL cc_start: 0.9059 (t) cc_final: 0.8762 (p)
REVERT: B  286 LYS cc_start: 0.8297 (ttmt) cc_final: 0.8081 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.1785
  time to fit residues: 34.1307
Evaluate side-chains
  89 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 90 optimal weight:    7.9990
   chunk 47 optimal weight:    1.9990
   chunk 54 optimal weight:    7.9990
   chunk 66 optimal weight:    8.9990
   chunk 29 optimal weight:    4.9990
   chunk 43 optimal weight:    0.0030
   chunk 77 optimal weight:    0.7980
   chunk 27 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   overall best weight:    0.9194

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

Flipped N/Q/H residues before XYZ refinement:
A 374 GLN
B 445 GLN
B 531 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.122570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.103211 restraints weight = 14972.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.103859 restraints weight = 11978.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.104598 restraints weight = 10497.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.1320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8832  Z= 0.201
  Angle     :  0.486   7.403  12028  Z= 0.257
  Chirality :  0.038   0.153   1374
  Planarity :  0.004   0.047   1496
  Dihedral  :  3.492  15.572   1166
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  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:  2.58 (0.26), residues: 1066
  helix:  2.52 (0.18), residues: 766
  sheet:  0.67 (0.92), residues: 48
  loop : -0.69 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 521 
 HIS   0.002   0.001   HIS B  58 
 PHE   0.014   0.001   PHE A  40 
 TYR   0.009   0.001   TYR A 234 
 ARG   0.004   0.000   ARG A 432 

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
REVERT: A  286 LYS cc_start: 0.8281 (ttmt) cc_final: 0.7952 (tppt)
REVERT: B   41 VAL cc_start: 0.9075 (t) cc_final: 0.8783 (p)
REVERT: B  286 LYS cc_start: 0.8378 (ttmt) cc_final: 0.8145 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.1720
  time to fit residues: 30.0922
Evaluate side-chains
  85 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 68 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 69 optimal weight:    5.9990
   chunk 99 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 531 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.126431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 84)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.106961 restraints weight = 14756.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.107879 restraints weight = 11950.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.108447 restraints weight = 10330.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.1492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8832  Z= 0.200
  Angle     :  0.490   7.217  12028  Z= 0.259
  Chirality :  0.038   0.150   1374
  Planarity :  0.004   0.044   1496
  Dihedral  :  3.560  15.568   1166
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  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:  2.44 (0.26), residues: 1066
  helix:  2.41 (0.18), residues: 766
  sheet:  0.66 (0.93), residues: 48
  loop : -0.74 (0.36), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 521 
 HIS   0.002   0.001   HIS A 401 
 PHE   0.011   0.001   PHE A  40 
 TYR   0.009   0.001   TYR B 234 
 ARG   0.006   0.000   ARG B 432 

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 1.019 
Fit side-chains
REVERT: A  286 LYS cc_start: 0.8265 (ttmt) cc_final: 0.7939 (tppt)
REVERT: B  286 LYS cc_start: 0.8264 (ttmt) cc_final: 0.8010 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.1759
  time to fit residues: 30.1867
Evaluate side-chains
  83 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 97 optimal weight:    0.8980
   chunk 85 optimal weight:    1.9990
   chunk 102 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 82 optimal weight:    0.6980
   chunk 14 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9980
   chunk 103 optimal weight:    1.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 531 ASN
** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.122671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.102836 restraints weight = 14646.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.103599 restraints weight = 12028.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.103896 restraints weight = 10524.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.1712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8832  Z= 0.256
  Angle     :  0.527   7.262  12028  Z= 0.284
  Chirality :  0.040   0.148   1374
  Planarity :  0.004   0.041   1496
  Dihedral  :  3.726  15.532   1166
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  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:  2.13 (0.25), residues: 1066
  helix:  2.20 (0.18), residues: 764
  sheet:  0.59 (0.95), residues: 48
  loop : -0.90 (0.36), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 521 
 HIS   0.003   0.001   HIS A 401 
 PHE   0.013   0.001   PHE A  40 
 TYR   0.011   0.001   TYR A 220 
 ARG   0.005   0.000   ARG B 432 

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.980 
Fit side-chains
   revert: symmetry clash
REVERT: A  122 MET cc_start: 0.8647 (ttm) cc_final: 0.8402 (ttm)
REVERT: A  286 LYS cc_start: 0.8312 (ttmt) cc_final: 0.7938 (tppt)
REVERT: B  122 MET cc_start: 0.8577 (ttm) cc_final: 0.8308 (ttm)
REVERT: B  286 LYS cc_start: 0.8316 (ttmt) cc_final: 0.7974 (tppt)
REVERT: B  521 TRP cc_start: 0.8808 (t60) cc_final: 0.8577 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.1652
  time to fit residues: 28.5772
Evaluate side-chains
  84 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 92 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9990
   chunk 52 optimal weight:    0.6980
   chunk 83 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 100 optimal weight:    0.7980
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 531 ASN
** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.126972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.107538 restraints weight = 14754.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.108465 restraints weight = 11804.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.108927 restraints weight = 10108.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.1802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   8832  Z= 0.185
  Angle     :  0.494   7.482  12028  Z= 0.261
  Chirality :  0.039   0.149   1374
  Planarity :  0.004   0.039   1496
  Dihedral  :  3.647  15.376   1166
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  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:  2.21 (0.26), residues: 1066
  helix:  2.27 (0.18), residues: 764
  sheet:  0.45 (0.93), residues: 48
  loop : -0.90 (0.36), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A  88 
 HIS   0.002   0.001   HIS A  25 
 PHE   0.010   0.001   PHE A 198 
 TYR   0.012   0.001   TYR B 234 
 ARG   0.004   0.000   ARG B 432 

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.855 
Fit side-chains
REVERT: A  286 LYS cc_start: 0.8251 (ttmt) cc_final: 0.7923 (tppt)
REVERT: B   41 VAL cc_start: 0.9076 (t) cc_final: 0.8793 (p)
REVERT: B  286 LYS cc_start: 0.8276 (ttmt) cc_final: 0.7980 (tppt)
REVERT: B  456 PRO cc_start: 0.8357 (Cg_exo) cc_final: 0.8152 (Cg_endo)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.1630
  time to fit residues: 29.7007
Evaluate side-chains
  84 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 63 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 11 optimal weight:    0.3980
   chunk 6 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 89 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** A 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 531 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.125897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.106348 restraints weight = 14813.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.107261 restraints weight = 12036.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.107756 restraints weight = 10424.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.1833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8832  Z= 0.209
  Angle     :  0.510   7.261  12028  Z= 0.271
  Chirality :  0.039   0.151   1374
  Planarity :  0.004   0.038   1496
  Dihedral  :  3.720  15.106   1166
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  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:  2.11 (0.25), residues: 1066
  helix:  2.19 (0.18), residues: 764
  sheet:  0.53 (0.93), residues: 48
  loop : -0.94 (0.36), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 521 
 HIS   0.002   0.001   HIS B 401 
 PHE   0.016   0.001   PHE B 187 
 TYR   0.007   0.001   TYR A 393 
 ARG   0.004   0.000   ARG B 432 

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.972 
Fit side-chains
REVERT: A  286 LYS cc_start: 0.8256 (ttmt) cc_final: 0.7934 (tppt)
REVERT: B  286 LYS cc_start: 0.8267 (ttmt) cc_final: 0.7985 (tppt)
REVERT: B  516 MET cc_start: 0.8943 (ptm) cc_final: 0.8741 (ptm)
  outliers start: 0
  outliers final: 0
  residues processed: 116
  average time/residue: 0.1720
  time to fit residues: 29.4280
Evaluate side-chains
  84 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9980
   chunk 88 optimal weight:    0.5980
   chunk 32 optimal weight:    5.9990
   chunk 44 optimal weight:    0.0370
   chunk 97 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 105 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 104 optimal weight:    0.8980
   overall best weight:    0.7058

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

Flipped N/Q/H residues before XYZ refinement:
** A 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 531 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.127720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.110246 restraints weight = 14505.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.110472 restraints weight = 11362.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.110440 restraints weight = 9355.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.1862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   8832  Z= 0.181
  Angle     :  0.498   7.416  12028  Z= 0.261
  Chirality :  0.039   0.171   1374
  Planarity :  0.004   0.038   1496
  Dihedral  :  3.649  15.093   1166
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  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:  2.17 (0.26), residues: 1066
  helix:  2.26 (0.18), residues: 764
  sheet:  0.45 (0.92), residues: 48
  loop : -0.96 (0.36), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 521 
 HIS   0.002   0.001   HIS A 143 
 PHE   0.010   0.001   PHE A 388 
 TYR   0.012   0.001   TYR B 234 
 ARG   0.003   0.000   ARG B 432 

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.913 
Fit side-chains
REVERT: A  286 LYS cc_start: 0.8231 (ttmt) cc_final: 0.7940 (tppt)
REVERT: B   41 VAL cc_start: 0.9038 (t) cc_final: 0.8747 (p)
REVERT: B  286 LYS cc_start: 0.8232 (ttmt) cc_final: 0.7981 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 116
  average time/residue: 0.1716
  time to fit residues: 29.4531
Evaluate side-chains
  85 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 101 optimal weight:    0.6980
   chunk 88 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   chunk 56 optimal weight:    4.9990
   chunk 73 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 103 optimal weight:    0.0370
   chunk 41 optimal weight:    0.6980
   chunk 105 optimal weight:    3.9990
   overall best weight:    0.6058

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

Flipped N/Q/H residues before XYZ refinement:
** A 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 531 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.128785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.110051 restraints weight = 14468.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.110829 restraints weight = 11056.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.111005 restraints weight = 9337.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.1891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   8832  Z= 0.166
  Angle     :  0.496   7.238  12028  Z= 0.257
  Chirality :  0.039   0.163   1374
  Planarity :  0.004   0.038   1496
  Dihedral  :  3.641  15.442   1166
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  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:  2.29 (0.26), residues: 1066
  helix:  2.34 (0.18), residues: 766
  sheet:  0.43 (0.92), residues: 48
  loop : -0.93 (0.36), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 521 
 HIS   0.004   0.001   HIS A 151 
 PHE   0.012   0.001   PHE A 198 
 TYR   0.009   0.001   TYR A 234 
 ARG   0.004   0.000   ARG B 432 

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.908 
Fit side-chains
REVERT: A  286 LYS cc_start: 0.8228 (ttmt) cc_final: 0.7932 (tppt)
REVERT: A  380 MET cc_start: 0.7543 (tpp) cc_final: 0.7268 (ttt)
REVERT: B   41 VAL cc_start: 0.9060 (t) cc_final: 0.8775 (p)
REVERT: B  286 LYS cc_start: 0.8214 (ttmt) cc_final: 0.7947 (tppt)
REVERT: B  380 MET cc_start: 0.7614 (tpp) cc_final: 0.7269 (ttt)
REVERT: B  446 ILE cc_start: 0.8422 (tp) cc_final: 0.7959 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.1666
  time to fit residues: 28.2529
Evaluate side-chains
  85 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 87 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   chunk 11 optimal weight:    4.9990
   chunk 63 optimal weight:    6.9990
   chunk 74 optimal weight:    0.1980
   chunk 82 optimal weight:    4.9990
   chunk 101 optimal weight:    0.8980
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
** A 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.124662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.105474 restraints weight = 14777.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.105942 restraints weight = 11935.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.106214 restraints weight = 10419.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.1986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   8832  Z= 0.238
  Angle     :  0.525   7.622  12028  Z= 0.278
  Chirality :  0.040   0.167   1374
  Planarity :  0.004   0.037   1496
  Dihedral  :  3.720  14.995   1166
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  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:  2.11 (0.26), residues: 1066
  helix:  2.22 (0.18), residues: 764
  sheet:  0.37 (0.92), residues: 48
  loop : -1.02 (0.36), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 521 
 HIS   0.002   0.001   HIS A 151 
 PHE   0.014   0.001   PHE B 187 
 TYR   0.008   0.001   TYR A 383 
 ARG   0.004   0.000   ARG B 432 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2480.50 seconds
wall clock time: 43 minutes 46.63 seconds (2626.63 seconds total)