Starting phenix.real_space_refine
on Fri Aug 22 23:40:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tpn_41478/08_2025/8tpn_41478.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tpn_41478/08_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_41478/08_2025/8tpn_41478.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tpn_41478/08_2025/8tpn_41478.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tpn_41478/08_2025/8tpn_41478.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tpn_41478/08_2025/8tpn_41478.cif"
  }
  resolution = 4.07
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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): 0.01s

  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: 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: {'GLU:plan': 9, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 4, 'ARG:plan': 4, 'TYR:plan': 1}
          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: 2.34, per 1000 atoms: 0.27
  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: 0.63
  Conformation dependent library (CDL) restraints added in 328.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.20
  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: 1.21

  Time building geometry restraints manager: 0.80 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: 0.02
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:             1.680
  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:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.340
  Find NCS groups from input model:        0.090
  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:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.630
-------------------------------------------------------------------------------
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= 0.111
  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 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:  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
 ARG   0.001   0.000   ARG B  45 
 TYR   0.009   0.001   TYR B 218 
 PHE   0.011   0.001   PHE A 187 
 TRP   0.015   0.001   TRP A 163 
 HIS   0.002   0.000   HIS B 611 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 8832)
  covalent geometry    : angle       0.46389 (12028)
  hydrogen bonds       : bond        0.14062 (  598)
  hydrogen bonds       : angle       4.66319 ( 1758)

*********************** 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  : 0.206 
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: 0.0652
  time to fit residues: 11.1416
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  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    0.3980
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    0.7980
   chunk 106 optimal weight:    0.6980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3493 r_free = 0.3493 target = 0.126311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.106845 restraints weight = 14732.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.107765 restraints weight = 11883.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.108361 restraints weight = 10250.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.108447 restraints weight = 9254.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.108527 restraints weight = 9077.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.0879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8832  Z= 0.118
  Angle     :  0.470   6.931  12028  Z= 0.251
  Chirality :  0.038   0.146   1374
  Planarity :  0.004   0.060   1496
  Dihedral  :  3.477  14.744   1166
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.77 (0.26), residues: 1066
  helix:  2.64 (0.18), residues: 766
  sheet:  0.67 (0.92), residues: 48
  loop : -0.54 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  45 
 TYR   0.007   0.001   TYR B 613 
 PHE   0.007   0.001   PHE A 198 
 TRP   0.012   0.001   TRP B 521 
 HIS   0.002   0.001   HIS A 127 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 8832)
  covalent geometry    : angle       0.47035 (12028)
  hydrogen bonds       : bond        0.04257 (  598)
  hydrogen bonds       : angle       3.40554 ( 1758)

*********************** 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
  121 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
REVERT: A  456 PRO cc_start: 0.8385 (Cg_exo) cc_final: 0.8143 (Cg_endo)
REVERT: B  456 PRO cc_start: 0.8370 (Cg_exo) cc_final: 0.8097 (Cg_endo)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.0717
  time to fit residues: 12.5630
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  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9980
   chunk 38 optimal weight:    0.0980
   chunk 53 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 90 optimal weight:    8.9990
   chunk 39 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 510 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 = 0.3403 r_free = 0.3403 target = 0.118788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.097796 restraints weight = 15284.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.098609 restraints weight = 12431.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.099373 restraints weight = 10742.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.099791 restraints weight = 9679.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.100134 restraints weight = 8981.915|
|-----------------------------------------------------------------------------|
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.1352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8832  Z= 0.159
  Angle     :  0.520   7.250  12028  Z= 0.278
  Chirality :  0.040   0.172   1374
  Planarity :  0.004   0.053   1496
  Dihedral  :  3.635  17.242   1166
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  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:  2.45 (0.26), residues: 1066
  helix:  2.40 (0.18), residues: 766
  sheet:  0.61 (0.92), residues: 48
  loop : -0.68 (0.36), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 432 
 TYR   0.011   0.002   TYR B 220 
 PHE   0.011   0.001   PHE B 198 
 TRP   0.017   0.001   TRP A 521 
 HIS   0.003   0.001   HIS B  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 8832)
  covalent geometry    : angle       0.51962 (12028)
  hydrogen bonds       : bond        0.05015 (  598)
  hydrogen bonds       : angle       3.40878 ( 1758)

*********************** 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
  119 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.342 
Fit side-chains
REVERT: A  122 MET cc_start: 0.8566 (ttm) cc_final: 0.8362 (ttm)
REVERT: A  286 LYS cc_start: 0.8289 (ttmt) cc_final: 0.7891 (tppt)
REVERT: B  122 MET cc_start: 0.8700 (ttm) cc_final: 0.8409 (ttm)
REVERT: B  286 LYS cc_start: 0.8397 (ttmt) cc_final: 0.8092 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.0686
  time to fit residues: 11.9832
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  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 107 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 103 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0170
   chunk 53 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 96 optimal weight:    0.5980
   overall best weight:    0.8822

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

Flipped N/Q/H residues before XYZ refinement:
B 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 = 0.3482 r_free = 0.3482 target = 0.125983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 92)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.106526 restraints weight = 14982.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.107244 restraints weight = 12078.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.108040 restraints weight = 10450.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.108387 restraints weight = 9356.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.108387 restraints weight = 8719.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.1484

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= 0.129
  Angle     :  0.493   7.236  12028  Z= 0.262
  Chirality :  0.039   0.154   1374
  Planarity :  0.004   0.047   1496
  Dihedral  :  3.622  15.635   1166
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  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:  2.36 (0.26), residues: 1066
  helix:  2.35 (0.18), residues: 766
  sheet:  0.62 (0.92), residues: 48
  loop : -0.76 (0.36), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 432 
 TYR   0.010   0.001   TYR A 234 
 PHE   0.010   0.001   PHE A  40 
 TRP   0.015   0.001   TRP A 521 
 HIS   0.002   0.001   HIS A 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 8832)
  covalent geometry    : angle       0.49258 (12028)
  hydrogen bonds       : bond        0.04431 (  598)
  hydrogen bonds       : angle       3.26282 ( 1758)

*********************** 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
  114 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.225 
Fit side-chains
REVERT: A  286 LYS cc_start: 0.8286 (ttmt) cc_final: 0.7892 (tppt)
REVERT: B  286 LYS cc_start: 0.8277 (ttmt) cc_final: 0.8030 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.0693
  time to fit residues: 11.6372
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  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 105 optimal weight:    2.9990
   chunk 80 optimal weight:    6.9990
   chunk 55 optimal weight:    5.9990
   chunk 106 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 77 optimal weight:    0.7980
   chunk 73 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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 374 GLN
B 531 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.120235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.101466 restraints weight = 14936.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.101986 restraints weight = 11083.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.101930 restraints weight = 9475.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.101970 restraints weight = 9274.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.102013 restraints weight = 9076.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.1673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   8832  Z= 0.153
  Angle     :  0.515   7.648  12028  Z= 0.275
  Chirality :  0.039   0.151   1374
  Planarity :  0.004   0.044   1496
  Dihedral  :  3.730  15.702   1166
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  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 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:  2.12 (0.25), residues: 1066
  helix:  2.16 (0.18), residues: 766
  sheet:  0.52 (0.93), residues: 48
  loop : -0.84 (0.36), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 432 
 TYR   0.010   0.001   TYR B 234 
 PHE   0.010   0.001   PHE B 375 
 TRP   0.017   0.001   TRP A 521 
 HIS   0.002   0.001   HIS A 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 8832)
  covalent geometry    : angle       0.51499 (12028)
  hydrogen bonds       : bond        0.04836 (  598)
  hydrogen bonds       : angle       3.34774 ( 1758)

*********************** 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
  111 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.283 
Fit side-chains
REVERT: A  286 LYS cc_start: 0.8292 (ttmt) cc_final: 0.7921 (tppt)
REVERT: B  286 LYS cc_start: 0.8330 (ttmt) cc_final: 0.7977 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.0649
  time to fit residues: 10.5219
Evaluate side-chains
  81 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 104 optimal weight:    0.9980
   chunk 35 optimal weight:    6.9990
   chunk 51 optimal weight:    0.0370
   chunk 58 optimal weight:    8.9990
   chunk 56 optimal weight:    7.9990
   chunk 88 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 90 optimal weight:    0.6980
   chunk 0 optimal weight:    5.9990
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.9260

-------------------------------------------------------------------------------
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 = 0.3468 r_free = 0.3468 target = 0.125189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.105523 restraints weight = 14833.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.106177 restraints weight = 12128.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.107001 restraints weight = 10607.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.107299 restraints weight = 9561.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.107544 restraints weight = 8966.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.1759

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= 0.132
  Angle     :  0.497   7.162  12028  Z= 0.264
  Chirality :  0.039   0.149   1374
  Planarity :  0.004   0.041   1496
  Dihedral  :  3.671  15.623   1166
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  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:  2.16 (0.26), residues: 1066
  helix:  2.23 (0.18), residues: 764
  sheet:  0.46 (0.93), residues: 48
  loop : -0.90 (0.36), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 432 
 TYR   0.012   0.001   TYR A 234 
 PHE   0.011   0.001   PHE B 187 
 TRP   0.015   0.001   TRP A 521 
 HIS   0.002   0.001   HIS A  25 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 8832)
  covalent geometry    : angle       0.49673 (12028)
  hydrogen bonds       : bond        0.04533 (  598)
  hydrogen bonds       : angle       3.27469 ( 1758)

*********************** 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  : 0.307 
Fit side-chains
   revert: symmetry clash
REVERT: A  286 LYS cc_start: 0.8291 (ttmt) cc_final: 0.7903 (tppt)
REVERT: B  286 LYS cc_start: 0.8293 (ttmt) cc_final: 0.7956 (tppt)
REVERT: B  456 PRO cc_start: 0.8340 (Cg_exo) cc_final: 0.8134 (Cg_endo)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.0691
  time to fit residues: 11.9166
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  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 7 optimal weight:    6.9990
   chunk 86 optimal weight:    3.9990
   chunk 24 optimal weight:    6.9990
   chunk 44 optimal weight:    0.7980
   chunk 88 optimal weight:    0.8980
   chunk 80 optimal weight:    3.9990
   chunk 103 optimal weight:    0.6980
   chunk 93 optimal weight:    4.9990
   chunk 94 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 90 optimal weight:    6.9990
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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 = 0.3464 r_free = 0.3464 target = 0.124522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 86)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.104823 restraints weight = 14899.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.105631 restraints weight = 12181.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.106379 restraints weight = 10454.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 16)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.106468 restraints weight = 9403.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.106865 restraints weight = 9151.072|
|-----------------------------------------------------------------------------|
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.1837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8832  Z= 0.141
  Angle     :  0.508   7.397  12028  Z= 0.271
  Chirality :  0.039   0.150   1374
  Planarity :  0.004   0.040   1496
  Dihedral  :  3.703  15.402   1166
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  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 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:  2.10 (0.26), residues: 1066
  helix:  2.18 (0.18), residues: 766
  sheet:  0.53 (0.92), residues: 48
  loop : -0.96 (0.36), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 432 
 TYR   0.010   0.001   TYR B 234 
 PHE   0.009   0.001   PHE A  40 
 TRP   0.018   0.001   TRP A 521 
 HIS   0.002   0.001   HIS A 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 8832)
  covalent geometry    : angle       0.50826 (12028)
  hydrogen bonds       : bond        0.04643 (  598)
  hydrogen bonds       : angle       3.31701 ( 1758)

*********************** 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
  115 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
REVERT: A  286 LYS cc_start: 0.8272 (ttmt) cc_final: 0.7895 (tppt)
REVERT: B  286 LYS cc_start: 0.8303 (ttmt) cc_final: 0.7959 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.0617
  time to fit residues: 10.6630
Evaluate side-chains
  81 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 22 optimal weight:    0.2980
   chunk 97 optimal weight:    1.9990
   chunk 109 optimal weight:   20.0000
   chunk 41 optimal weight:    0.6980
   chunk 0 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9980
   chunk 50 optimal weight:    0.8980
   chunk 92 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9990
   chunk 62 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.3483 r_free = 0.3483 target = 0.126143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.108071 restraints weight = 14660.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.108581 restraints weight = 11015.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.108541 restraints weight = 8910.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.108564 restraints weight = 8913.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.108595 restraints weight = 8820.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.1849

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= 0.123
  Angle     :  0.490   6.994  12028  Z= 0.259
  Chirality :  0.038   0.149   1374
  Planarity :  0.004   0.038   1496
  Dihedral  :  3.666  15.479   1166
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  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:  2.19 (0.26), residues: 1066
  helix:  2.28 (0.18), residues: 764
  sheet:  0.49 (0.92), residues: 48
  loop : -1.00 (0.36), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 432 
 TYR   0.012   0.001   TYR A 234 
 PHE   0.009   0.001   PHE A  40 
 TRP   0.017   0.001   TRP A 521 
 HIS   0.005   0.001   HIS A 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 8832)
  covalent geometry    : angle       0.48995 (12028)
  hydrogen bonds       : bond        0.04333 (  598)
  hydrogen bonds       : angle       3.23068 ( 1758)

*********************** 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
  112 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.326 
Fit side-chains
REVERT: A  286 LYS cc_start: 0.8198 (ttmt) cc_final: 0.7906 (tppt)
REVERT: B  286 LYS cc_start: 0.8263 (ttmt) cc_final: 0.7976 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.0804
  time to fit residues: 13.1510
Evaluate side-chains
  82 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 3 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 89 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 23 optimal weight:    4.9990
   chunk 87 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 105 optimal weight:    1.9990
   chunk 22 optimal weight:    0.4980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3490 r_free = 0.3490 target = 0.126903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 84)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.107568 restraints weight = 14622.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.108415 restraints weight = 11925.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.108971 restraints weight = 10277.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.109434 restraints weight = 9307.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.109434 restraints weight = 8738.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.1856

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= 0.126
  Angle     :  0.503   7.362  12028  Z= 0.264
  Chirality :  0.039   0.171   1374
  Planarity :  0.004   0.038   1496
  Dihedral  :  3.654  15.155   1166
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  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 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:  2.19 (0.26), residues: 1066
  helix:  2.26 (0.18), residues: 768
  sheet:  0.45 (0.91), residues: 48
  loop : -0.97 (0.36), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 432 
 TYR   0.011   0.001   TYR B 234 
 PHE   0.016   0.001   PHE A 187 
 TRP   0.017   0.001   TRP A 521 
 HIS   0.003   0.001   HIS A 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 8832)
  covalent geometry    : angle       0.50329 (12028)
  hydrogen bonds       : bond        0.04333 (  598)
  hydrogen bonds       : angle       3.25684 ( 1758)

*********************** 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
  109 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A  286 LYS cc_start: 0.8228 (ttmt) cc_final: 0.7911 (tppt)
REVERT: B  286 LYS cc_start: 0.8254 (ttmt) cc_final: 0.7974 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.0800
  time to fit residues: 13.0148
Evaluate side-chains
  82 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 102 optimal weight:    0.0470
   chunk 77 optimal weight:    0.4980
   chunk 99 optimal weight:    0.9980
   chunk 89 optimal weight:    0.8980
   chunk 64 optimal weight:    0.5980
   chunk 97 optimal weight:    2.9990
   chunk 33 optimal weight:    0.5980
   chunk 74 optimal weight:    0.6980
   chunk 59 optimal weight:    4.9990
   chunk 70 optimal weight:    0.7980
   chunk 1 optimal weight:    5.9990
   overall best weight:    0.4878

-------------------------------------------------------------------------------
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 = 0.3458 r_free = 0.3458 target = 0.123721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.103701 restraints weight = 14656.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.104643 restraints weight = 11680.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.105399 restraints weight = 9975.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.105755 restraints weight = 8955.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.105755 restraints weight = 8363.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.1928

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= 0.107
  Angle     :  0.485   7.229  12028  Z= 0.252
  Chirality :  0.038   0.164   1374
  Planarity :  0.004   0.038   1496
  Dihedral  :  3.578  15.655   1166
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  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 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:  2.35 (0.26), residues: 1066
  helix:  2.40 (0.18), residues: 766
  sheet:  0.37 (0.90), residues: 48
  loop : -0.93 (0.36), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 432 
 TYR   0.009   0.001   TYR A 613 
 PHE   0.011   0.001   PHE B 187 
 TRP   0.016   0.001   TRP A 521 
 HIS   0.005   0.001   HIS B 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 8832)
  covalent geometry    : angle       0.48482 (12028)
  hydrogen bonds       : bond        0.03868 (  598)
  hydrogen bonds       : angle       3.15091 ( 1758)

********************** 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
  107 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.327 
Fit side-chains
REVERT: A  286 LYS cc_start: 0.8217 (ttmt) cc_final: 0.7919 (tppt)
REVERT: B   41 VAL cc_start: 0.9048 (t) cc_final: 0.8753 (p)
REVERT: B  286 LYS cc_start: 0.8210 (ttmt) cc_final: 0.7956 (tppt)
REVERT: B  380 MET cc_start: 0.7575 (tpp) cc_final: 0.7353 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.0806
  time to fit residues: 12.7147
Evaluate side-chains
  82 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 74 optimal weight:    0.6980
   chunk 101 optimal weight:    0.7980
   chunk 11 optimal weight:    5.9990
   chunk 90 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 85 optimal weight:    0.9980
   chunk 28 optimal weight:    0.2980
   chunk 17 optimal weight:    1.9990
   chunk 86 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3452 r_free = 0.3452 target = 0.123232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.104605 restraints weight = 14699.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.105397 restraints weight = 10817.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.105125 restraints weight = 8727.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.105224 restraints weight = 9253.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.105235 restraints weight = 8785.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.1894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8832  Z= 0.114
  Angle     :  0.481   7.298  12028  Z= 0.252
  Chirality :  0.038   0.165   1374
  Planarity :  0.004   0.038   1496
  Dihedral  :  3.568  14.790   1166
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  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 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:  2.31 (0.26), residues: 1066
  helix:  2.37 (0.18), residues: 768
  sheet:  0.36 (0.91), residues: 48
  loop : -0.97 (0.36), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 432 
 TYR   0.010   0.001   TYR A 234 
 PHE   0.012   0.001   PHE B 187 
 TRP   0.016   0.001   TRP A 521 
 HIS   0.002   0.001   HIS B 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 8832)
  covalent geometry    : angle       0.48056 (12028)
  hydrogen bonds       : bond        0.03997 (  598)
  hydrogen bonds       : angle       3.17434 ( 1758)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1235.18 seconds
wall clock time: 22 minutes 1.92 seconds (1321.92 seconds total)