Starting phenix.real_space_refine
on Sat Aug 23 01:22:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8chb_16659/08_2025/8chb_16659_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8chb_16659/08_2025/8chb_16659.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.14
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8chb_16659/08_2025/8chb_16659.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8chb_16659/08_2025/8chb_16659.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8chb_16659/08_2025/8chb_16659_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8chb_16659/08_2025/8chb_16659_neut.cif"
  }
  resolution = 3.14
  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=   0.018
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: 4
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    5716      2.51       5
     N    1486      2.21       5
     O    1678      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 56 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: 8916
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4458
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 579, 4458
          Classifications: {'peptide': 579}
          Link IDs: {'PTRANS': 17, 'TRANS': 561}
    Chain: "B"
      Number of atoms: 4458
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 579, 4458
          Classifications: {'peptide': 579}
          Link IDs: {'PTRANS': 17, 'TRANS': 561}
  Time building chain proxies: 2.07, per 1000 atoms: 0.23
  Number of scatterers: 8916
  At special positions: 0
  Unit cell: (108.07, 73.83, 138.03, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      36     16.00
     O    1678      8.00
     N    1486      7.00
     C    5716      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 582 " - pdb=" SG  CYS B 582 " distance=1.94

  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: 0.87
  Conformation dependent library (CDL) restraints added in 352.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2132

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 4 sheets defined
      63.7% alpha, 6.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 21
      removed outlier: 3.527A  pdb=" N   ALA A  17 " --> pdb=" O   LYS A  13 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 26 through 44
    Processing helix  chain 'A' and resid 45 through 56
    Processing helix  chain 'A' and resid 64 through 109
      removed outlier: 3.879A  pdb=" N   LYS A 109 " --> pdb=" O   LYS A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 117
    Processing helix  chain 'A' and resid 120 through 140
      removed outlier: 4.356A  pdb=" N   THR A 131 " --> pdb=" O   VAL A 127 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   MET A 132 " --> pdb=" O   THR A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 162
    Processing helix  chain 'A' and resid 164 through 210
      Proline residue:  A 175  - end of helix
      Proline residue:  A 183  - end of helix
    Processing helix  chain 'A' and resid 213 through 219
    Processing helix  chain 'A' and resid 222 through 274
      removed outlier: 3.635A  pdb=" N   GLY A 232 " --> pdb=" O   ARG A 228 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   LEU A 249 " --> pdb=" O   LYS A 245 " (cutoff:3.500A)
      Proline residue:  A 252  - end of helix
    Processing helix  chain 'A' and resid 280 through 295
      removed outlier: 3.746A  pdb=" N   GLN A 292 " --> pdb=" O   LEU A 288 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   MET A 295 " --> pdb=" O   PHE A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 322
      removed outlier: 3.517A  pdb=" N   THR A 302 " --> pdb=" O   GLY A 298 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   PHE A 304 " --> pdb=" O   ILE A 300 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   THR A 305 " --> pdb=" O   THR A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 388
      removed outlier: 3.724A  pdb=" N   PHE A 384 " --> pdb=" O   LYS A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 416
      removed outlier: 3.832A  pdb=" N   HIS A 416 " --> pdb=" O   SER A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 436
    Processing helix  chain 'A' and resid 447 through 454
      removed outlier: 4.925A  pdb=" N   MET A 454 " --> pdb=" O   LYS A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 462
    Processing helix  chain 'A' and resid 481 through 495
    Processing helix  chain 'A' and resid 514 through 525
      removed outlier: 4.066A  pdb=" N   VAL A 523 " --> pdb=" O   GLN A 519 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   LEU A 524 " --> pdb=" O   ALA A 520 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   MET A 525 " --> pdb=" O   LEU A 521 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 537 through 540
    Processing helix  chain 'A' and resid 560 through 565
    Processing helix  chain 'A' and resid 569 through 579
      removed outlier: 4.118A  pdb=" N   ALA A 574 " --> pdb=" O   TYR A 570 " (cutoff:3.500A)
      removed outlier: 5.920A  pdb=" N   GLN A 577 " --> pdb=" O   PHE A 573 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 12 through 21
      removed outlier: 3.527A  pdb=" N   ALA B  17 " --> pdb=" O   LYS B  13 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 26 through 44
    Processing helix  chain 'B' and resid 45 through 56
    Processing helix  chain 'B' and resid 64 through 109
      removed outlier: 3.880A  pdb=" N   LYS B 109 " --> pdb=" O   LYS B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 113 through 117
    Processing helix  chain 'B' and resid 120 through 140
      removed outlier: 4.356A  pdb=" N   THR B 131 " --> pdb=" O   VAL B 127 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   MET B 132 " --> pdb=" O   THR B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 162
    Processing helix  chain 'B' and resid 164 through 210
      Proline residue:  B 175  - end of helix
      Proline residue:  B 183  - end of helix
    Processing helix  chain 'B' and resid 213 through 219
    Processing helix  chain 'B' and resid 222 through 274
      removed outlier: 3.635A  pdb=" N   GLY B 232 " --> pdb=" O   ARG B 228 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   LEU B 249 " --> pdb=" O   LYS B 245 " (cutoff:3.500A)
      Proline residue:  B 252  - end of helix
    Processing helix  chain 'B' and resid 280 through 295
      removed outlier: 3.747A  pdb=" N   GLN B 292 " --> pdb=" O   LEU B 288 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   MET B 295 " --> pdb=" O   PHE B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 296 through 322
      removed outlier: 3.518A  pdb=" N   THR B 302 " --> pdb=" O   GLY B 298 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   PHE B 304 " --> pdb=" O   ILE B 300 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   THR B 305 " --> pdb=" O   THR B 301 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 380 through 388
      removed outlier: 3.724A  pdb=" N   PHE B 384 " --> pdb=" O   LYS B 380 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 436
    Processing helix  chain 'B' and resid 410 through 416
      removed outlier: 3.832A  pdb=" N   HIS B 416 " --> pdb=" O   SER B 412 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 447 through 454
      removed outlier: 4.925A  pdb=" N   MET B 454 " --> pdb=" O   LYS B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 457 through 462
    Processing helix  chain 'B' and resid 481 through 495
    Processing helix  chain 'B' and resid 514 through 525
      removed outlier: 4.067A  pdb=" N   VAL B 523 " --> pdb=" O   GLN B 519 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   LEU B 524 " --> pdb=" O   ALA B 520 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   MET B 525 " --> pdb=" O   LEU B 521 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 537 through 540
    Processing helix  chain 'B' and resid 560 through 565
    Processing helix  chain 'B' and resid 569 through 579
      removed outlier: 4.118A  pdb=" N   ALA B 574 " --> pdb=" O   TYR B 570 " (cutoff:3.500A)
      removed outlier: 5.921A  pdb=" N   GLN B 577 " --> pdb=" O   PHE B 573 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 357 through 364
      removed outlier: 6.471A  pdb=" N   LYS B 358 " --> pdb=" O   SER B 347 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   SER B 347 " --> pdb=" O   LYS B 358 " (cutoff:3.500A)
      removed outlier: 5.390A  pdb=" N   VAL B 360 " --> pdb=" O   ARG B 345 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   THR B 397 " --> pdb=" O   ASP B 344 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 417 through 421
      removed outlier: 6.503A  pdb=" N   GLY B 418 " --> pdb=" O   MET B 501 " (cutoff:3.500A)
      removed outlier: 8.107A  pdb=" N   ASP B 503 " --> pdb=" O   GLY B 418 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   VAL B 420 " --> pdb=" O   ASP B 503 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   LEU B 500 " --> pdb=" O   ILE B 531 " (cutoff:3.500A)
      removed outlier: 7.959A  pdb=" N   ILE B 533 " --> pdb=" O   LEU B 500 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   LEU B 502 " --> pdb=" O   ILE B 533 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   VAL B 369 " --> pdb=" O   GLN B 545 " (cutoff:3.500A)
      removed outlier: 8.263A  pdb=" N   LEU B 547 " --> pdb=" O   VAL B 369 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   ALA B 371 " --> pdb=" O   LEU B 547 " (cutoff:3.500A)
      removed outlier: 7.995A  pdb=" N   VAL B 549 " --> pdb=" O   ALA B 371 " (cutoff:3.500A)
      removed outlier: 8.482A  pdb=" N   VAL B 373 " --> pdb=" O   VAL B 549 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 357 through 364
      removed outlier: 6.470A  pdb=" N   LYS A 358 " --> pdb=" O   SER A 347 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   SER A 347 " --> pdb=" O   LYS A 358 " (cutoff:3.500A)
      removed outlier: 5.390A  pdb=" N   VAL A 360 " --> pdb=" O   ARG A 345 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   THR A 397 " --> pdb=" O   ASP A 344 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 417 through 421
      removed outlier: 6.503A  pdb=" N   GLY A 418 " --> pdb=" O   MET A 501 " (cutoff:3.500A)
      removed outlier: 8.108A  pdb=" N   ASP A 503 " --> pdb=" O   GLY A 418 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   VAL A 420 " --> pdb=" O   ASP A 503 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   LEU A 500 " --> pdb=" O   ILE A 531 " (cutoff:3.500A)
      removed outlier: 7.959A  pdb=" N   ILE A 533 " --> pdb=" O   LEU A 500 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   LEU A 502 " --> pdb=" O   ILE A 533 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   VAL A 369 " --> pdb=" O   GLN A 545 " (cutoff:3.500A)
      removed outlier: 8.264A  pdb=" N   LEU A 547 " --> pdb=" O   VAL A 369 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   ALA A 371 " --> pdb=" O   LEU A 547 " (cutoff:3.500A)
      removed outlier: 7.995A  pdb=" N   VAL A 549 " --> pdb=" O   ALA A 371 " (cutoff:3.500A)
      removed outlier: 8.482A  pdb=" N   VAL A 373 " --> pdb=" O   VAL A 549 " (cutoff:3.500A)

    532 hydrogen bonds defined for protein.
    1584 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: 1.48

  Time building geometry restraints manager: 1.12 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1600
        1.31 -     1.44: 2077
        1.44 -     1.56: 5303
        1.56 -     1.69: 0
        1.69 -     1.82: 70
  Bond restraints: 9050
  Sorted by residual:
  bond pdb=" CZ  ARG A 228 "
       pdb=" NH2 ARG A 228 "
    ideal  model  delta    sigma   weight residual
    1.330  1.254  0.076 1.30e-02 5.92e+03 3.44e+01
  bond pdb=" CZ  ARG B 228 "
       pdb=" NH2 ARG B 228 "
    ideal  model  delta    sigma   weight residual
    1.330  1.254  0.076 1.30e-02 5.92e+03 3.40e+01
  bond pdb=" C   THR A 555 "
       pdb=" O   THR A 555 "
    ideal  model  delta    sigma   weight residual
    1.235  1.187  0.049 9.00e-03 1.23e+04 2.93e+01
  bond pdb=" C   THR B 555 "
       pdb=" O   THR B 555 "
    ideal  model  delta    sigma   weight residual
    1.235  1.187  0.048 9.00e-03 1.23e+04 2.84e+01
  bond pdb=" C   ASN A 207 "
       pdb=" O   ASN A 207 "
    ideal  model  delta    sigma   weight residual
    1.236  1.188  0.049 1.15e-02 7.56e+03 1.80e+01
  ... (remaining 9045 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.39: 10262
        2.39 -     4.78: 1808
        4.78 -     7.18: 170
        7.18 -     9.57: 4
        9.57 -    11.96: 2
  Bond angle restraints: 12246
  Sorted by residual:
  angle pdb=" N   PHE A 304 "
        pdb=" CA  PHE A 304 "
        pdb=" C   PHE A 304 "
      ideal   model   delta    sigma   weight residual
     111.36  117.90   -6.54 1.09e+00 8.42e-01 3.60e+01
  angle pdb=" N   PHE B 304 "
        pdb=" CA  PHE B 304 "
        pdb=" C   PHE B 304 "
      ideal   model   delta    sigma   weight residual
     111.36  117.89   -6.53 1.09e+00 8.42e-01 3.59e+01
  angle pdb=" N   ASN B 207 "
        pdb=" CA  ASN B 207 "
        pdb=" C   ASN B 207 "
      ideal   model   delta    sigma   weight residual
     110.97  104.55    6.42 1.09e+00 8.42e-01 3.47e+01
  angle pdb=" N   ASN A 207 "
        pdb=" CA  ASN A 207 "
        pdb=" C   ASN A 207 "
      ideal   model   delta    sigma   weight residual
     110.97  104.59    6.38 1.09e+00 8.42e-01 3.43e+01
  angle pdb=" N   ARG A 571 "
        pdb=" CA  ARG A 571 "
        pdb=" C   ARG A 571 "
      ideal   model   delta    sigma   weight residual
     111.69  104.99    6.70 1.23e+00 6.61e-01 2.97e+01
  ... (remaining 12241 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.03: 4905
       17.03 -    34.07: 430
       34.07 -    51.10: 98
       51.10 -    68.13: 36
       68.13 -    85.16: 18
  Dihedral angle restraints: 5487
    sinusoidal: 2169
      harmonic: 3318
  Sorted by residual:
  dihedral pdb=" CA  ILE A 364 "
           pdb=" C   ILE A 364 "
           pdb=" N   GLU A 365 "
           pdb=" CA  GLU A 365 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.17  -27.83     0      5.00e+00 4.00e-02 3.10e+01
  dihedral pdb=" CA  ILE B 364 "
           pdb=" C   ILE B 364 "
           pdb=" N   GLU B 365 "
           pdb=" CA  GLU B 365 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.20  -27.80     0      5.00e+00 4.00e-02 3.09e+01
  dihedral pdb=" CA  GLN A 342 "
           pdb=" C   GLN A 342 "
           pdb=" N   LEU A 343 "
           pdb=" CA  LEU A 343 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.87   27.13     0      5.00e+00 4.00e-02 2.94e+01
  ... (remaining 5484 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 952
       0.069 -    0.138: 358
       0.138 -    0.207: 120
       0.207 -    0.276: 42
       0.276 -    0.346: 8
  Chirality restraints: 1480
  Sorted by residual:
  chirality pdb=" CA  SER B 507 "
            pdb=" N   SER B 507 "
            pdb=" C   SER B 507 "
            pdb=" CB  SER B 507 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 2.99e+00
  chirality pdb=" CA  SER A 507 "
            pdb=" N   SER A 507 "
            pdb=" C   SER A 507 "
            pdb=" CB  SER A 507 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.97e+00
  chirality pdb=" CB  THR B 555 "
            pdb=" CA  THR B 555 "
            pdb=" OG1 THR B 555 "
            pdb=" CG2 THR B 555 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.21    0.34 2.00e-01 2.50e+01 2.89e+00
  ... (remaining 1477 not shown)

  Planarity restraints: 1540
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 268 "   -0.087 2.00e-02 2.50e+03   4.82e-02 4.64e+01
        pdb=" CG  TYR B 268 "    0.027 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 268 "    0.032 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 268 "    0.045 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 268 "    0.032 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 268 "    0.022 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 268 "    0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR B 268 "   -0.075 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 268 "    0.087 2.00e-02 2.50e+03   4.80e-02 4.61e+01
        pdb=" CG  TYR A 268 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 268 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 268 "   -0.045 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 268 "   -0.032 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 268 "   -0.021 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 268 "   -0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR A 268 "    0.075 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 413 "    0.060 2.00e-02 2.50e+03   3.55e-02 3.14e+01
        pdb=" CG  TRP B 413 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 413 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 413 "   -0.027 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 413 "   -0.039 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 413 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 413 "   -0.052 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 413 "    0.040 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 413 "   -0.014 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 413 "    0.045 2.00e-02 2.50e+03
  ... (remaining 1537 not shown)

  Histogram of nonbonded interaction distances:
        2.51 -     2.99: 4447
        2.99 -     3.47: 9701
        3.47 -     3.94: 13930
        3.94 -     4.42: 15782
        4.42 -     4.90: 25564
  Nonbonded interactions: 69424
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 437 "
            pdb=" OE2 GLU B 225 "
     model   vdw
     2.512 3.040
  nonbonded pdb=" OG  SER A 428 "
            pdb=" NE2 GLN B 208 "
     model   vdw
     2.521 3.120
  nonbonded pdb=" O   VAL B 182 "
            pdb=" CA  PRO B 183 "
     model   vdw
     2.533 2.776
  nonbonded pdb=" O   VAL A 182 "
            pdb=" CA  PRO A 183 "
     model   vdw
     2.533 2.776
  nonbonded pdb=" O   GLY B 298 "
            pdb=" OG1 THR B 301 "
     model   vdw
     2.537 3.040
  ... (remaining 69419 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.810
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.170
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7507
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      :  0.012   0.105   9051  Z= 0.801
  Angle     :  1.750  11.960  12248  Z= 1.186
  Chirality :  0.088   0.346   1480
  Planarity :  0.013   0.157   1540
  Dihedral  : 15.261  85.163   3352
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  :  8.18 %
    Favored  : 90.18 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.52 (0.22), residues: 1154
  helix: -0.72 (0.17), residues: 748
  sheet:  0.40 (0.74), residues: 54
  loop : -1.55 (0.29), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.040   0.002   ARG B 214 
 TYR   0.087   0.012   TYR B 268 
 PHE   0.055   0.006   PHE A 286 
 TRP   0.060   0.014   TRP B 413 
 HIS   0.012   0.003   HIS B 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.01230 ( 9050)
  covalent geometry    : angle       1.74754 (12246)
  SS BOND              : bond        0.08851 (    1)
  SS BOND              : angle       6.82564 (    2)
  hydrogen bonds       : bond        0.19099 (  532)
  hydrogen bonds       : angle       7.07436 ( 1584)

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 129
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8541 (mm)
REVERT: A  390 PHE cc_start: 0.7410 (t80) cc_final: 0.6988 (t80)
REVERT: A  391 TYR cc_start: 0.7864 (m-80) cc_final: 0.7605 (m-10)
REVERT: A  427 MET cc_start: 0.8154 (mmt) cc_final: 0.7682 (mmt)
REVERT: B  390 PHE cc_start: 0.7384 (t80) cc_final: 0.7045 (t80)
REVERT: B  391 TYR cc_start: 0.7907 (m-10) cc_final: 0.7649 (m-10)
REVERT: B  427 MET cc_start: 0.8100 (mmt) cc_final: 0.7724 (mmt)
  outliers start: 16
  outliers final: 6
  residues processed: 143
  average time/residue: 0.1067
  time to fit residues: 20.6603
Evaluate side-chains
  85 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 78
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  319 GLU
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  571 ARG
Chi-restraints excluded: chain B residue  319 GLU
Chi-restraints excluded: chain B residue  532 VAL
Chi-restraints excluded: chain B residue  571 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    0.4980
   chunk 113 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 208 GLN
A 292 GLN
B 208 GLN
B 292 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.165238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.130407 restraints weight = 13417.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.3795 rms_B_bonded: 2.32
r_work: 0.3597 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.2204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9051  Z= 0.167
  Angle     :  0.684   6.400  12248  Z= 0.360
  Chirality :  0.043   0.190   1480
  Planarity :  0.005   0.043   1540
  Dihedral  :  5.860  42.296   1256
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 11.55 %
    Favored  : 87.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.84 (0.24), residues: 1154
  helix:  1.28 (0.19), residues: 746
  sheet:  1.00 (0.69), residues: 54
  loop : -1.04 (0.30), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 228 
 TYR   0.012   0.001   TYR A 456 
 PHE   0.019   0.002   PHE A 390 
 TRP   0.007   0.002   TRP B 164 
 HIS   0.005   0.002   HIS A 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 9050)
  covalent geometry    : angle       0.68366 (12246)
  SS BOND              : bond        0.00484 (    1)
  SS BOND              : angle       0.15792 (    2)
  hydrogen bonds       : bond        0.05869 (  532)
  hydrogen bonds       : angle       4.62234 ( 1584)

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.346 
Fit side-chains
REVERT: A  188 MET cc_start: 0.7990 (tmm) cc_final: 0.7622 (tmm)
REVERT: A  529 THR cc_start: 0.7528 (m) cc_final: 0.6723 (p)
REVERT: B  188 MET cc_start: 0.8012 (tmm) cc_final: 0.7628 (tmm)
REVERT: B  368 LYS cc_start: 0.6893 (OUTLIER) cc_final: 0.6656 (ttmm)
REVERT: B  427 MET cc_start: 0.8084 (mmt) cc_final: 0.7817 (mmt)
REVERT: B  529 THR cc_start: 0.7465 (m) cc_final: 0.6724 (p)
  outliers start: 12
  outliers final: 10
  residues processed: 102
  average time/residue: 0.0809
  time to fit residues: 12.0709
Evaluate side-chains
  80 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 69
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  493 LEU
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain B residue  368 LYS
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain B residue  530 THR
Chi-restraints excluded: chain B residue  532 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 11 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 59 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 101 optimal weight:    0.0970
   overall best weight:    0.6778

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.164589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.129234 restraints weight = 13437.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.3806 rms_B_bonded: 2.47
r_work: 0.3612 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.2663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9051  Z= 0.140
  Angle     :  0.586   7.288  12248  Z= 0.309
  Chirality :  0.040   0.158   1480
  Planarity :  0.004   0.031   1540
  Dihedral  :  4.789  21.910   1240
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 12.68 %
    Favored  : 85.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.56 (0.25), residues: 1154
  helix:  1.85 (0.19), residues: 750
  sheet:  1.57 (0.72), residues: 54
  loop : -0.86 (0.31), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 228 
 TYR   0.010   0.001   TYR B 391 
 PHE   0.017   0.001   PHE B 390 
 TRP   0.010   0.002   TRP A 164 
 HIS   0.003   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 9050)
  covalent geometry    : angle       0.58593 (12246)
  SS BOND              : bond        0.00497 (    1)
  SS BOND              : angle       0.36771 (    2)
  hydrogen bonds       : bond        0.04962 (  532)
  hydrogen bonds       : angle       4.21599 ( 1584)

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 74
  time to evaluate  : 0.396 
Fit side-chains
REVERT: A  188 MET cc_start: 0.7982 (tmm) cc_final: 0.7667 (tmm)
REVERT: A  529 THR cc_start: 0.7455 (m) cc_final: 0.6619 (p)
REVERT: A  580 MET cc_start: 0.6441 (ttt) cc_final: 0.6028 (ttt)
REVERT: B  188 MET cc_start: 0.8002 (tmm) cc_final: 0.7688 (tmm)
REVERT: B  358 LYS cc_start: 0.8383 (tptp) cc_final: 0.7964 (mmmm)
REVERT: B  427 MET cc_start: 0.7983 (mmt) cc_final: 0.7740 (mmt)
REVERT: B  529 THR cc_start: 0.7470 (m) cc_final: 0.6696 (p)
  outliers start: 21
  outliers final: 13
  residues processed: 89
  average time/residue: 0.0797
  time to fit residues: 10.5038
Evaluate side-chains
  77 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 MET
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain B residue   59 MET
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  417 ILE
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  530 THR
Chi-restraints excluded: chain B residue  532 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 63 optimal weight:    0.5980
   chunk 51 optimal weight:    0.2980
   chunk 52 optimal weight:    0.9990
   chunk 64 optimal weight:    0.6980
   chunk 69 optimal weight:    3.9990
   chunk 27 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 60 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 76 optimal weight:    2.9990
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.164225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.129095 restraints weight = 13538.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.3795 rms_B_bonded: 2.34
r_work: 0.3604 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.2964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9051  Z= 0.133
  Angle     :  0.568   8.883  12248  Z= 0.290
  Chirality :  0.039   0.154   1480
  Planarity :  0.003   0.030   1540
  Dihedral  :  4.593  20.959   1240
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 13.29 %
    Favored  : 84.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.85 (0.25), residues: 1154
  helix:  2.15 (0.19), residues: 736
  sheet:  0.93 (0.66), residues: 72
  loop : -0.76 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 528 
 TYR   0.007   0.001   TYR A 456 
 PHE   0.014   0.001   PHE A 390 
 TRP   0.010   0.001   TRP A 164 
 HIS   0.003   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 9050)
  covalent geometry    : angle       0.56776 (12246)
  SS BOND              : bond        0.00474 (    1)
  SS BOND              : angle       0.47081 (    2)
  hydrogen bonds       : bond        0.04557 (  532)
  hydrogen bonds       : angle       4.01011 ( 1584)

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 66
  time to evaluate  : 0.350 
Fit side-chains
REVERT: A  580 MET cc_start: 0.6572 (ttt) cc_final: 0.6266 (ttt)
REVERT: B  188 MET cc_start: 0.7973 (tmm) cc_final: 0.7656 (tmm)
REVERT: B  580 MET cc_start: 0.6947 (ttt) cc_final: 0.6637 (ttt)
  outliers start: 20
  outliers final: 14
  residues processed: 82
  average time/residue: 0.0822
  time to fit residues: 10.2585
Evaluate side-chains
  78 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain B residue  162 MET
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  417 ILE
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  530 THR
Chi-restraints excluded: chain B residue  532 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 107 optimal weight:    8.9990
   chunk 101 optimal weight:    0.9990
   chunk 106 optimal weight:    3.9990
   chunk 62 optimal weight:    0.2980
   chunk 6 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 58 optimal weight:    0.4980
   chunk 82 optimal weight:    0.5980
   chunk 39 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   overall best weight:    0.6182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.163838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.129151 restraints weight = 13510.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3813 rms_B_bonded: 2.34
r_work: 0.3622 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.3181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9051  Z= 0.127
  Angle     :  0.557   7.663  12248  Z= 0.288
  Chirality :  0.040   0.181   1480
  Planarity :  0.003   0.030   1540
  Dihedral  :  4.455  19.303   1240
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 14.83 %
    Favored  : 83.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.00 (0.25), residues: 1154
  helix:  2.23 (0.20), residues: 740
  sheet:  1.95 (0.74), residues: 54
  loop : -0.72 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 557 
 TYR   0.024   0.001   TYR A 408 
 PHE   0.031   0.001   PHE A 390 
 TRP   0.011   0.001   TRP A 164 
 HIS   0.003   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 9050)
  covalent geometry    : angle       0.55734 (12246)
  SS BOND              : bond        0.00459 (    1)
  SS BOND              : angle       0.52890 (    2)
  hydrogen bonds       : bond        0.04293 (  532)
  hydrogen bonds       : angle       3.85337 ( 1584)

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 72
  time to evaluate  : 0.361 
Fit side-chains
REVERT: A  580 MET cc_start: 0.6565 (ttt) cc_final: 0.6336 (ttt)
REVERT: B  580 MET cc_start: 0.6891 (ttt) cc_final: 0.6518 (ttt)
  outliers start: 17
  outliers final: 15
  residues processed: 84
  average time/residue: 0.0810
  time to fit residues: 10.4059
Evaluate side-chains
  82 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 67
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 MET
Chi-restraints excluded: chain A residue  162 MET
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain B residue  162 MET
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  417 ILE
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  532 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 94 optimal weight:    0.9980
   chunk 113 optimal weight:    9.9990
   chunk 28 optimal weight:    0.0060
   chunk 83 optimal weight:    1.9990
   chunk 106 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 44 optimal weight:    0.8980
   chunk 93 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 63 optimal weight:    0.6980
   overall best weight:    0.6196

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.164060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.129742 restraints weight = 13618.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.3796 rms_B_bonded: 2.31
r_work: 0.3610 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start:          0.3378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9051  Z= 0.125
  Angle     :  0.549   8.155  12248  Z= 0.281
  Chirality :  0.039   0.152   1480
  Planarity :  0.003   0.028   1540
  Dihedral  :  4.371  19.115   1240
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 15.95 %
    Favored  : 81.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.07 (0.26), residues: 1154
  helix:  2.33 (0.20), residues: 738
  sheet:  1.17 (0.69), residues: 72
  loop : -0.77 (0.32), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 345 
 TYR   0.007   0.001   TYR A 350 
 PHE   0.037   0.001   PHE B 390 
 TRP   0.011   0.001   TRP A 164 
 HIS   0.003   0.001   HIS A 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 9050)
  covalent geometry    : angle       0.54913 (12246)
  SS BOND              : bond        0.00441 (    1)
  SS BOND              : angle       0.49726 (    2)
  hydrogen bonds       : bond        0.04143 (  532)
  hydrogen bonds       : angle       3.76144 ( 1584)

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 69
  time to evaluate  : 0.376 
Fit side-chains
  outliers start: 22
  outliers final: 17
  residues processed: 87
  average time/residue: 0.0862
  time to fit residues: 11.1472
Evaluate side-chains
  82 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 65
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  162 MET
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  162 MET
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  530 THR
Chi-restraints excluded: chain B residue  532 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0670
   chunk 47 optimal weight:    0.8980
   chunk 76 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 94 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   chunk 27 optimal weight:    0.8980
   chunk 96 optimal weight:    1.9990
   overall best weight:    0.6718

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.163544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.128760 restraints weight = 13578.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3792 rms_B_bonded: 2.40
r_work: 0.3595 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.3492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9051  Z= 0.130
  Angle     :  0.546   8.538  12248  Z= 0.278
  Chirality :  0.039   0.156   1480
  Planarity :  0.003   0.028   1540
  Dihedral  :  4.336  18.922   1240
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 15.85 %
    Favored  : 81.49 %
  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:  2.07 (0.26), residues: 1154
  helix:  2.41 (0.20), residues: 738
  sheet:  1.14 (0.70), residues: 72
  loop : -0.97 (0.31), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 345 
 TYR   0.006   0.001   TYR B 456 
 PHE   0.037   0.001   PHE A 390 
 TRP   0.012   0.002   TRP A 164 
 HIS   0.002   0.001   HIS B 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 9050)
  covalent geometry    : angle       0.54650 (12246)
  SS BOND              : bond        0.00364 (    1)
  SS BOND              : angle       0.31265 (    2)
  hydrogen bonds       : bond        0.04145 (  532)
  hydrogen bonds       : angle       3.73575 ( 1584)

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 65
  time to evaluate  : 0.372 
Fit side-chains
REVERT: A  580 MET cc_start: 0.6726 (ttt) cc_final: 0.6274 (ttt)
REVERT: B  168 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8130 (mp)
  outliers start: 26
  outliers final: 18
  residues processed: 86
  average time/residue: 0.0801
  time to fit residues: 10.5393
Evaluate side-chains
  81 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 62
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 MET
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  162 MET
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  162 MET
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  407 THR
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  530 THR
Chi-restraints excluded: chain B residue  532 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 113 optimal weight:    9.9990
   chunk 65 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 83 optimal weight:    0.7980
   chunk 96 optimal weight:    1.9990
   chunk 84 optimal weight:    0.8980
   chunk 87 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   overall best weight:    1.1182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.161507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.125808 restraints weight = 13681.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3742 rms_B_bonded: 2.51
r_work: 0.3546 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.3599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9051  Z= 0.175
  Angle     :  0.612   9.966  12248  Z= 0.305
  Chirality :  0.041   0.153   1480
  Planarity :  0.004   0.032   1540
  Dihedral  :  4.459  21.264   1240
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 15.54 %
    Favored  : 81.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.88 (0.26), residues: 1154
  helix:  2.27 (0.20), residues: 742
  sheet:  0.33 (0.82), residues: 52
  loop : -0.83 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 100 
 TYR   0.009   0.001   TYR B 456 
 PHE   0.039   0.001   PHE A 390 
 TRP   0.016   0.002   TRP A 164 
 HIS   0.003   0.001   HIS A 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 9050)
  covalent geometry    : angle       0.61237 (12246)
  SS BOND              : bond        0.00352 (    1)
  SS BOND              : angle       0.34169 (    2)
  hydrogen bonds       : bond        0.04564 (  532)
  hydrogen bonds       : angle       3.89180 ( 1584)

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 63
  time to evaluate  : 0.363 
Fit side-chains
REVERT: A  222 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7392 (mm-30)
REVERT: A  231 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.8092 (mmm)
REVERT: A  580 MET cc_start: 0.6753 (ttt) cc_final: 0.6400 (ttt)
REVERT: B  580 MET cc_start: 0.6436 (ttt) cc_final: 0.5747 (ppp)
  outliers start: 27
  outliers final: 17
  residues processed: 84
  average time/residue: 0.0829
  time to fit residues: 10.6411
Evaluate side-chains
  80 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 61
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 MET
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  162 MET
Chi-restraints excluded: chain A residue  222 GLU
Chi-restraints excluded: chain A residue  231 MET
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  162 MET
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  417 ILE
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  530 THR
Chi-restraints excluded: chain B residue  532 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 85 optimal weight:    0.9980
   chunk 57 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9990
   chunk 79 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 71 optimal weight:    0.0970
   chunk 32 optimal weight:    0.3980
   chunk 15 optimal weight:    0.5980
   chunk 92 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.163384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.128658 restraints weight = 13604.479|
|-----------------------------------------------------------------------------|
r_work (start): 0.3783 rms_B_bonded: 2.45
r_work: 0.3586 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.3720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9051  Z= 0.125
  Angle     :  0.563   9.060  12248  Z= 0.282
  Chirality :  0.039   0.156   1480
  Planarity :  0.003   0.029   1540
  Dihedral  :  4.294  19.467   1240
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 16.16 %
    Favored  : 81.90 %
  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:  2.01 (0.26), residues: 1154
  helix:  2.39 (0.20), residues: 742
  sheet:  0.14 (0.81), residues: 52
  loop : -0.78 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 345 
 TYR   0.006   0.001   TYR A  90 
 PHE   0.038   0.001   PHE A 390 
 TRP   0.017   0.002   TRP B 164 
 HIS   0.003   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 9050)
  covalent geometry    : angle       0.56299 (12246)
  SS BOND              : bond        0.00383 (    1)
  SS BOND              : angle       0.50671 (    2)
  hydrogen bonds       : bond        0.04144 (  532)
  hydrogen bonds       : angle       3.71571 ( 1584)

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 68
  time to evaluate  : 0.352 
Fit side-chains
REVERT: A  222 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7345 (mm-30)
REVERT: A  580 MET cc_start: 0.6752 (ttt) cc_final: 0.6410 (ttt)
REVERT: B  168 LEU cc_start: 0.8458 (mt) cc_final: 0.8227 (mt)
REVERT: B  222 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7264 (mm-30)
REVERT: B  231 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.8090 (mmm)
REVERT: B  580 MET cc_start: 0.6418 (ttt) cc_final: 0.5774 (ppp)
  outliers start: 19
  outliers final: 14
  residues processed: 81
  average time/residue: 0.0771
  time to fit residues: 9.4847
Evaluate side-chains
  84 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 67
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  162 MET
Chi-restraints excluded: chain A residue  222 GLU
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  162 MET
Chi-restraints excluded: chain B residue  222 GLU
Chi-restraints excluded: chain B residue  231 MET
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  530 THR
Chi-restraints excluded: chain B residue  532 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 98 optimal weight:    0.6980
   chunk 14 optimal weight:    0.5980
   chunk 106 optimal weight:    2.9990
   chunk 105 optimal weight:    0.0670
   chunk 84 optimal weight:    0.7980
   chunk 27 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9980
   chunk 110 optimal weight:    3.9990
   overall best weight:    0.5718

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.163914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.129146 restraints weight = 13535.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3787 rms_B_bonded: 2.47
r_work: 0.3593 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.3847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9051  Z= 0.120
  Angle     :  0.564   9.756  12248  Z= 0.279
  Chirality :  0.039   0.157   1480
  Planarity :  0.003   0.029   1540
  Dihedral  :  4.158  17.993   1239
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 15.95 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.13 (0.26), residues: 1154
  helix:  2.52 (0.20), residues: 738
  sheet: -0.07 (0.78), residues: 52
  loop : -0.74 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 345 
 TYR   0.005   0.001   TYR B 456 
 PHE   0.037   0.001   PHE A 390 
 TRP   0.014   0.002   TRP B 164 
 HIS   0.003   0.001   HIS B 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 9050)
  covalent geometry    : angle       0.56363 (12246)
  SS BOND              : bond        0.00341 (    1)
  SS BOND              : angle       0.54527 (    2)
  hydrogen bonds       : bond        0.03978 (  532)
  hydrogen bonds       : angle       3.63686 ( 1584)

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 76
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
REVERT: A  222 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7234 (mm-30)
REVERT: A  580 MET cc_start: 0.6732 (ttt) cc_final: 0.6447 (ttt)
REVERT: B  168 LEU cc_start: 0.8316 (mt) cc_final: 0.8008 (mt)
REVERT: B  222 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7236 (mm-30)
REVERT: B  427 MET cc_start: 0.7779 (mmt) cc_final: 0.7158 (mmt)
REVERT: B  580 MET cc_start: 0.6327 (ttt) cc_final: 0.5595 (ppp)
  outliers start: 19
  outliers final: 16
  residues processed: 89
  average time/residue: 0.0847
  time to fit residues: 11.3301
Evaluate side-chains
  89 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 71
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 MET
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  162 MET
Chi-restraints excluded: chain A residue  222 GLU
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain B residue   59 MET
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  162 MET
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  222 GLU
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  530 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 42 optimal weight:    0.4980
   chunk 25 optimal weight:    0.6980
   chunk 46 optimal weight:    8.9990
   chunk 96 optimal weight:    0.9980
   chunk 57 optimal weight:    4.9990
   chunk 35 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 67 optimal weight:    0.0870
   chunk 20 optimal weight:    0.8980
   chunk 73 optimal weight:    0.1980
   chunk 52 optimal weight:    0.0770
   overall best weight:    0.3116

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

Flipped N/Q/H residues before XYZ refinement:
** B 141 HIS ** 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 = 0.4243 r_free = 0.4243 target = 0.163436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.128275 restraints weight = 13568.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.3810 rms_B_bonded: 2.36
r_work: 0.3619 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.3943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.056   9051  Z= 0.108
  Angle     :  0.551   9.194  12248  Z= 0.280
  Chirality :  0.038   0.159   1480
  Planarity :  0.003   0.030   1540
  Dihedral  :  4.042  17.198   1238
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 16.16 %
    Favored  : 82.21 %
  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:  2.27 (0.26), residues: 1154
  helix:  2.62 (0.19), residues: 738
  sheet: -0.19 (0.77), residues: 52
  loop : -0.66 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 389 
 TYR   0.005   0.001   TYR A  90 
 PHE   0.035   0.001   PHE A 390 
 TRP   0.013   0.001   TRP B 164 
 HIS   0.003   0.001   HIS A 567 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 9050)
  covalent geometry    : angle       0.55112 (12246)
  SS BOND              : bond        0.00347 (    1)
  SS BOND              : angle       0.57216 (    2)
  hydrogen bonds       : bond        0.03773 (  532)
  hydrogen bonds       : angle       3.51658 ( 1584)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2016.47 seconds
wall clock time: 35 minutes 23.67 seconds (2123.67 seconds total)