Starting phenix.real_space_refine
on Tue Mar  3 22:42:46 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7psd_13612/03_2026/7psd_13612.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7psd_13612/03_2026/7psd_13612.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7psd_13612/03_2026/7psd_13612.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7psd_13612/03_2026/7psd_13612.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7psd_13612/03_2026/7psd_13612.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7psd_13612/03_2026/7psd_13612.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.102
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      24      5.16       5
     C    5784      2.51       5
     N    1574      2.21       5
     O    1650      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 66 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9032
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      Number of atoms: 4516
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 580, 4516
          Classifications: {'peptide': 580}
          Link IDs: {'PTRANS': 17, 'TRANS': 562}
  Restraints were copied for chains:
    A
  Time building chain proxies: 3.47, per 1000 atoms: 0.38
  Number of scatterers: 9032
  At special positions: 0
  Unit cell: (118.976, 75.712, 141.44, 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      24     16.00
     O    1650      8.00
     N    1574      7.00
     C    5784      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: 0.70
  Conformation dependent library (CDL) restraints added in 363.8 milliseconds
  

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2164

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 6 sheets defined
      69.2% alpha, 7.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'B' and resid 95 through 103
      removed outlier: 3.669A  pdb=" N   GLN B  99 " --> pdb=" O   ALA B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 145
      Proline residue:  B 134  - end of helix
    Processing helix  chain 'B' and resid 159 through 206
      removed outlier: 3.750A  pdb=" N   GLN B 177 " --> pdb=" O   ALA B 173 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   SER B 186 " --> pdb=" O   ALA B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 213
    Processing helix  chain 'B' and resid 217 through 240
    Processing helix  chain 'B' and resid 240 through 259
    Processing helix  chain 'B' and resid 260 through 309
      removed outlier: 3.824A  pdb=" N   ALA B 264 " --> pdb=" O   GLY B 260 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   THR B 286 " --> pdb=" O   THR B 282 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   LYS B 287 " --> pdb=" O   ALA B 283 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   PHE B 288 " --> pdb=" O   TRP B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 309 through 316
    Processing helix  chain 'B' and resid 318 through 371
      removed outlier: 3.504A  pdb=" N   GLU B 322 " --> pdb=" O   ASN B 318 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   SER B 336 " --> pdb=" O   ALA B 332 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   LYS B 339 " --> pdb=" O   ARG B 335 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 391
      removed outlier: 3.662A  pdb=" N   LEU B 380 " --> pdb=" O   SER B 376 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   VAL B 381 " --> pdb=" O   VAL B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 392 through 398
      removed outlier: 4.270A  pdb=" N   ASN B 395 " --> pdb=" O   VAL B 392 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   PHE B 396 " --> pdb=" O   PRO B 393 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LEU B 397 " --> pdb=" O   LEU B 394 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   GLY B 398 " --> pdb=" O   ASN B 395 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 392 through 398'
    Processing helix  chain 'B' and resid 399 through 418
      removed outlier: 3.742A  pdb=" N   ARG B 405 " --> pdb=" O   TYR B 401 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LEU B 414 " --> pdb=" O   ASP B 410 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 481 through 488
      removed outlier: 4.653A  pdb=" N   ARG B 485 " --> pdb=" O   SER B 481 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 509 through 516
    Processing helix  chain 'B' and resid 531 through 537
    Processing helix  chain 'B' and resid 543 through 554
    Processing helix  chain 'B' and resid 556 through 563
    Processing helix  chain 'B' and resid 565 through 568
      removed outlier: 4.052A  pdb=" N   GLN B 568 " --> pdb=" O   HIS B 565 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 565 through 568'
    Processing helix  chain 'B' and resid 579 through 595
    Processing helix  chain 'B' and resid 603 through 607
      removed outlier: 3.937A  pdb=" N   ALA B 607 " --> pdb=" O   ALA B 604 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 609 through 625
    Processing helix  chain 'B' and resid 637 through 642
      removed outlier: 3.922A  pdb=" N   TYR B 642 " --> pdb=" O   ARG B 639 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 661 through 666
      removed outlier: 3.554A  pdb=" N   GLU B 666 " --> pdb=" O   ARG B 662 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 670 through 674
      removed outlier: 4.033A  pdb=" N   GLU B 673 " --> pdb=" O   VAL B 670 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 103
    Processing helix  chain 'A' and resid 110 through 145
      Proline residue:  A 134  - end of helix
    Processing helix  chain 'A' and resid 159 through 206
      removed outlier: 3.749A  pdb=" N   GLN A 177 " --> pdb=" O   ALA A 173 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   SER A 186 " --> pdb=" O   ALA A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 213
    Processing helix  chain 'A' and resid 217 through 240
    Processing helix  chain 'A' and resid 240 through 259
    Processing helix  chain 'A' and resid 260 through 309
      removed outlier: 3.823A  pdb=" N   ALA A 264 " --> pdb=" O   GLY A 260 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   THR A 286 " --> pdb=" O   THR A 282 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   LYS A 287 " --> pdb=" O   ALA A 283 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   PHE A 288 " --> pdb=" O   TRP A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 316
    Processing helix  chain 'A' and resid 318 through 371
      removed outlier: 3.504A  pdb=" N   GLU A 322 " --> pdb=" O   ASN A 318 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   SER A 336 " --> pdb=" O   ALA A 332 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   LYS A 339 " --> pdb=" O   ARG A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 391
      removed outlier: 3.661A  pdb=" N   LEU A 380 " --> pdb=" O   SER A 376 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   VAL A 381 " --> pdb=" O   VAL A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 398
      removed outlier: 4.271A  pdb=" N   ASN A 395 " --> pdb=" O   VAL A 392 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   PHE A 396 " --> pdb=" O   PRO A 393 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LEU A 397 " --> pdb=" O   LEU A 394 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   GLY A 398 " --> pdb=" O   ASN A 395 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 392 through 398'
    Processing helix  chain 'A' and resid 399 through 418
      removed outlier: 3.743A  pdb=" N   ARG A 405 " --> pdb=" O   TYR A 401 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LEU A 414 " --> pdb=" O   ASP A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 488
      removed outlier: 4.653A  pdb=" N   ARG A 485 " --> pdb=" O   SER A 481 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 516
    Processing helix  chain 'A' and resid 531 through 537
    Processing helix  chain 'A' and resid 543 through 554
    Processing helix  chain 'A' and resid 556 through 563
    Processing helix  chain 'A' and resid 565 through 568
      removed outlier: 4.052A  pdb=" N   GLN A 568 " --> pdb=" O   HIS A 565 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 565 through 568'
    Processing helix  chain 'A' and resid 579 through 595
    Processing helix  chain 'A' and resid 603 through 607
      removed outlier: 3.937A  pdb=" N   ALA A 607 " --> pdb=" O   ALA A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 609 through 625
    Processing helix  chain 'A' and resid 637 through 642
      removed outlier: 3.923A  pdb=" N   TYR A 642 " --> pdb=" O   ARG A 639 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 661 through 666
      removed outlier: 3.555A  pdb=" N   GLU A 666 " --> pdb=" O   ARG A 662 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 670 through 674
      removed outlier: 4.034A  pdb=" N   GLU A 673 " --> pdb=" O   VAL A 670 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 457 through 464
      removed outlier: 5.296A  pdb=" N   ARG B 458 " --> pdb=" O   PHE B 448 " (cutoff:3.500A)
      removed outlier: 7.274A  pdb=" N   PHE B 448 " --> pdb=" O   ARG B 458 " (cutoff:3.500A)
      removed outlier: 7.286A  pdb=" N   LEU B 462 " --> pdb=" O   GLU B 444 " (cutoff:3.500A)
      removed outlier: 5.258A  pdb=" N   GLU B 444 " --> pdb=" O   LEU B 462 " (cutoff:3.500A)
      removed outlier: 7.490A  pdb=" N   ILE B 464 " --> pdb=" O   ARG B 442 " (cutoff:3.500A)
      removed outlier: 5.641A  pdb=" N   ARG B 442 " --> pdb=" O   ILE B 464 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   VAL B 446 " --> pdb=" O   GLN B 495 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   GLN B 495 " --> pdb=" O   VAL B 446 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 517 through 519
      removed outlier: 3.556A  pdb=" N   ILE B 647 " --> pdb=" O   GLY B 659 " (cutoff:3.500A)
      removed outlier: 4.723A  pdb=" N   GLU B 657 " --> pdb=" O   VAL B 649 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 529 through 530
    Processing sheet with id=AA4, first strand: chain 'A' and resid 457 through 464
      removed outlier: 5.296A  pdb=" N   ARG A 458 " --> pdb=" O   PHE A 448 " (cutoff:3.500A)
      removed outlier: 7.274A  pdb=" N   PHE A 448 " --> pdb=" O   ARG A 458 " (cutoff:3.500A)
      removed outlier: 7.285A  pdb=" N   LEU A 462 " --> pdb=" O   GLU A 444 " (cutoff:3.500A)
      removed outlier: 5.259A  pdb=" N   GLU A 444 " --> pdb=" O   LEU A 462 " (cutoff:3.500A)
      removed outlier: 7.490A  pdb=" N   ILE A 464 " --> pdb=" O   ARG A 442 " (cutoff:3.500A)
      removed outlier: 5.640A  pdb=" N   ARG A 442 " --> pdb=" O   ILE A 464 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   VAL A 446 " --> pdb=" O   GLN A 495 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   GLN A 495 " --> pdb=" O   VAL A 446 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 517 through 519
      removed outlier: 3.556A  pdb=" N   ILE A 647 " --> pdb=" O   GLY A 659 " (cutoff:3.500A)
      removed outlier: 4.723A  pdb=" N   GLU A 657 " --> pdb=" O   VAL A 649 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 529 through 530

    612 hydrogen bonds defined for protein.
    1800 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: 1.40

  Time building geometry restraints manager: 0.95 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2635
        1.33 -     1.45: 1694
        1.45 -     1.58: 4823
        1.58 -     1.70: 0
        1.70 -     1.82: 44
  Bond restraints: 9196
  Sorted by residual:
  bond pdb=" CB  THR A 281 "
       pdb=" CG2 THR A 281 "
    ideal  model  delta    sigma   weight residual
    1.521  1.391  0.130 3.30e-02 9.18e+02 1.54e+01
  bond pdb=" CB  THR B 281 "
       pdb=" CG2 THR B 281 "
    ideal  model  delta    sigma   weight residual
    1.521  1.392  0.129 3.30e-02 9.18e+02 1.53e+01
  bond pdb=" C   SER B 156 "
       pdb=" N   ALA B 157 "
    ideal  model  delta    sigma   weight residual
    1.332  1.287  0.046 1.40e-02 5.10e+03 1.07e+01
  bond pdb=" C   SER A 156 "
       pdb=" N   ALA A 157 "
    ideal  model  delta    sigma   weight residual
    1.332  1.288  0.045 1.40e-02 5.10e+03 1.03e+01
  bond pdb=" CG1 ILE A 192 "
       pdb=" CD1 ILE A 192 "
    ideal  model  delta    sigma   weight residual
    1.513  1.392  0.121 3.90e-02 6.57e+02 9.60e+00
  ... (remaining 9191 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.56: 11973
        2.56 -     5.13: 436
        5.13 -     7.69: 47
        7.69 -    10.25: 10
       10.25 -    12.81: 4
  Bond angle restraints: 12470
  Sorted by residual:
  angle pdb=" CA  TRP A 284 "
        pdb=" CB  TRP A 284 "
        pdb=" CG  TRP A 284 "
      ideal   model   delta    sigma   weight residual
     113.60  121.87   -8.27 1.90e+00 2.77e-01 1.89e+01
  angle pdb=" CA  TRP B 284 "
        pdb=" CB  TRP B 284 "
        pdb=" CG  TRP B 284 "
      ideal   model   delta    sigma   weight residual
     113.60  121.84   -8.24 1.90e+00 2.77e-01 1.88e+01
  angle pdb=" N   VAL B 400 "
        pdb=" CA  VAL B 400 "
        pdb=" C   VAL B 400 "
      ideal   model   delta    sigma   weight residual
     110.36  114.48   -4.12 1.05e+00 9.07e-01 1.54e+01
  angle pdb=" N   VAL A 400 "
        pdb=" CA  VAL A 400 "
        pdb=" C   VAL A 400 "
      ideal   model   delta    sigma   weight residual
     110.36  114.48   -4.12 1.05e+00 9.07e-01 1.54e+01
  angle pdb=" N   VAL B 155 "
        pdb=" CA  VAL B 155 "
        pdb=" C   VAL B 155 "
      ideal   model   delta    sigma   weight residual
     110.21  105.89    4.32 1.13e+00 7.83e-01 1.46e+01
  ... (remaining 12465 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.12: 4918
       17.12 -    34.24: 485
       34.24 -    51.36: 89
       51.36 -    68.48: 10
       68.48 -    85.59: 14
  Dihedral angle restraints: 5516
    sinusoidal: 2156
      harmonic: 3360
  Sorted by residual:
  dihedral pdb=" CA  TYR A 451 "
           pdb=" C   TYR A 451 "
           pdb=" N   PRO A 452 "
           pdb=" CA  PRO A 452 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.36  -25.64     0      5.00e+00 4.00e-02 2.63e+01
  dihedral pdb=" CA  TYR B 451 "
           pdb=" C   TYR B 451 "
           pdb=" N   PRO B 452 "
           pdb=" CA  PRO B 452 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.39  -25.61     0      5.00e+00 4.00e-02 2.62e+01
  dihedral pdb=" CA  SER B 399 "
           pdb=" C   SER B 399 "
           pdb=" N   VAL B 400 "
           pdb=" CA  VAL B 400 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.21  -22.79     0      5.00e+00 4.00e-02 2.08e+01
  ... (remaining 5513 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.118: 1365
       0.118 -    0.235: 97
       0.235 -    0.353: 0
       0.353 -    0.470: 0
       0.470 -    0.588: 2
  Chirality restraints: 1464
  Sorted by residual:
  chirality pdb=" CB  ILE A 192 "
            pdb=" CA  ILE A 192 "
            pdb=" CG1 ILE A 192 "
            pdb=" CG2 ILE A 192 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.06    0.59 2.00e-01 2.50e+01 8.63e+00
  chirality pdb=" CB  ILE B 192 "
            pdb=" CA  ILE B 192 "
            pdb=" CG1 ILE B 192 "
            pdb=" CG2 ILE B 192 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.06    0.59 2.00e-01 2.50e+01 8.61e+00
  chirality pdb=" CA  PHE A 355 "
            pdb=" N   PHE A 355 "
            pdb=" C   PHE A 355 "
            pdb=" CB  PHE A 355 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.36e+00
  ... (remaining 1461 not shown)

  Planarity restraints: 1584
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 137 "    0.015 2.00e-02 2.50e+03   2.54e-02 1.13e+01
        pdb=" CG  PHE A 137 "   -0.053 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 137 "    0.032 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 137 "    0.011 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 137 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 137 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 137 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 137 "   -0.015 2.00e-02 2.50e+03   2.52e-02 1.11e+01
        pdb=" CG  PHE B 137 "    0.053 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 137 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 137 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 137 "    0.015 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 137 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 137 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 388 "   -0.031 2.00e-02 2.50e+03   1.97e-02 6.78e+00
        pdb=" CG  PHE B 388 "    0.034 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 388 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 388 "    0.015 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 388 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 388 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 388 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1581 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 454
        2.70 -     3.25: 9435
        3.25 -     3.80: 14950
        3.80 -     4.35: 18651
        4.35 -     4.90: 31686
  Nonbonded interactions: 75176
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 566 "
            pdb=" OG1 THR A 569 "
     model   vdw
     2.146 3.040
  nonbonded pdb=" O   GLY B 566 "
            pdb=" OG1 THR B 569 "
     model   vdw
     2.146 3.040
  nonbonded pdb=" O   LEU A 586 "
            pdb=" OG  SER A 589 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" O   LEU B 586 "
            pdb=" OG  SER B 589 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" O   ARG B 637 "
            pdb=" OG1 THR B 640 "
     model   vdw
     2.302 3.040
  ... (remaining 75171 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 'B'
  selection = chain 'A'
}

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:             2.190
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     11.010
  Find NCS groups from input model:        0.070
  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:6.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
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      :  0.015   0.130   9196  Z= 0.619
  Angle     :  1.115  12.813  12470  Z= 0.626
  Chirality :  0.069   0.588   1464
  Planarity :  0.006   0.056   1584
  Dihedral  : 14.392  85.594   3352
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  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 are not related in a simple way.
  whole: -1.38 (0.23), residues: 1156
  helix: -0.59 (0.17), residues: 750
  sheet: -0.63 (0.68), residues: 56
  loop : -1.37 (0.35), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 170 
 TYR   0.017   0.003   TYR A 401 
 PHE   0.053   0.005   PHE A 137 
 TRP   0.037   0.005   TRP B 284 
 HIS   0.004   0.001   HIS A 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.01502 ( 9196)
  covalent geometry    : angle       1.11533 (12470)
  hydrogen bonds       : bond        0.14069 (  612)
  hydrogen bonds       : angle       6.27969 ( 1800)

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.269 
Fit side-chains
REVERT: B  468 LYS cc_start: 0.7532 (mmmm) cc_final: 0.7306 (mmpt)
REVERT: B  621 ASN cc_start: 0.9158 (m-40) cc_final: 0.8475 (m110)
REVERT: B  632 LEU cc_start: 0.8247 (mp) cc_final: 0.7948 (mp)
  outliers start: 0
  outliers final: 1
  residues processed: 123
  average time/residue: 0.3928
  time to fit residues: 52.9888
Evaluate side-chains
  103 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 102
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 108 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:   10.0000
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.5980
   chunk 100 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 205 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.207643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.123169 restraints weight = 9578.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 1.87
r_work: 0.3314 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3171 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.1371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9196  Z= 0.150
  Angle     :  0.627   7.428  12470  Z= 0.336
  Chirality :  0.043   0.171   1464
  Planarity :  0.004   0.045   1584
  Dihedral  :  5.124  22.680   1268
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 10.71 %
    Favored  : 88.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.08 (0.25), residues: 1156
  helix:  0.64 (0.18), residues: 754
  sheet: -0.46 (0.67), residues: 56
  loop : -0.99 (0.37), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 221 
 TYR   0.009   0.001   TYR A 232 
 PHE   0.032   0.003   PHE B 388 
 TRP   0.022   0.002   TRP A 284 
 HIS   0.002   0.001   HIS B 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 9196)
  covalent geometry    : angle       0.62676 (12470)
  hydrogen bonds       : bond        0.05050 (  612)
  hydrogen bonds       : angle       4.48570 ( 1800)

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 0.346 
Fit side-chains
REVERT: B  232 TYR cc_start: 0.8661 (t80) cc_final: 0.8448 (t80)
REVERT: B  632 LEU cc_start: 0.8015 (mp) cc_final: 0.7747 (mp)
REVERT: A  305 ASP cc_start: 0.7999 (t70) cc_final: 0.7734 (t0)
REVERT: A  416 ASP cc_start: 0.7841 (m-30) cc_final: 0.7528 (p0)
REVERT: A  595 ASP cc_start: 0.8007 (t0) cc_final: 0.7554 (p0)
  outliers start: 12
  outliers final: 5
  residues processed: 113
  average time/residue: 0.3004
  time to fit residues: 38.2289
Evaluate side-chains
  94 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 89
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  556 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 54 optimal weight:    7.9990
   chunk 56 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9990
   chunk 113 optimal weight:   20.0000
   chunk 75 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 107 optimal weight:    3.9990
   chunk 82 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 69 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
** B 503 GLN ** 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 = 0.4369 r_free = 0.4369 target = 0.205899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.118234 restraints weight = 9725.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.3413 rms_B_bonded: 1.94
r_work: 0.3278 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3133 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.1603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   9196  Z= 0.205
  Angle     :  0.623   7.429  12470  Z= 0.332
  Chirality :  0.044   0.164   1464
  Planarity :  0.004   0.039   1584
  Dihedral  :  4.854  20.785   1268
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 13.51 %
    Favored  : 83.99 %
  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 are not related in a simple way.
  whole:  0.50 (0.25), residues: 1156
  helix:  1.01 (0.18), residues: 756
  sheet:  0.01 (0.86), residues: 36
  loop : -0.97 (0.35), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 138 
 TYR   0.011   0.001   TYR B 136 
 PHE   0.031   0.002   PHE B 388 
 TRP   0.018   0.002   TRP B 284 
 HIS   0.003   0.001   HIS A 555 

Details of bonding type rmsd
  covalent geometry    : bond        0.00495 ( 9196)
  covalent geometry    : angle       0.62311 (12470)
  hydrogen bonds       : bond        0.05180 (  612)
  hydrogen bonds       : angle       4.44890 ( 1800)

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 93
  time to evaluate  : 0.332 
Fit side-chains
REVERT: B  632 LEU cc_start: 0.7933 (mp) cc_final: 0.7681 (mp)
REVERT: B  657 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.7017 (pm20)
REVERT: A  441 ILE cc_start: 0.8865 (mt) cc_final: 0.8474 (mm)
REVERT: A  595 ASP cc_start: 0.8076 (t0) cc_final: 0.7606 (p0)
REVERT: A  657 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7308 (pm20)
  outliers start: 24
  outliers final: 11
  residues processed: 108
  average time/residue: 0.3721
  time to fit residues: 44.7660
Evaluate side-chains
  102 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  301 THR
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  657 GLU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  293 ASN
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain A residue  657 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 27 optimal weight:    0.5980
   chunk 94 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   chunk 99 optimal weight:    8.9990
   chunk 20 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 113 optimal weight:    0.9980
   chunk 90 optimal weight:    1.9990
   chunk 57 optimal weight:    6.9990
   chunk 65 optimal weight:    0.5980
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 503 GLN ** 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 = 0.4372 r_free = 0.4372 target = 0.207957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.119718 restraints weight = 9778.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.3419 rms_B_bonded: 2.01
r_work: 0.3279 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3131 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.1911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9196  Z= 0.146
  Angle     :  0.574   8.128  12470  Z= 0.305
  Chirality :  0.042   0.155   1464
  Planarity :  0.003   0.033   1584
  Dihedral  :  4.635  19.638   1268
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.97 %
    Favored  : 82.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.91 (0.25), residues: 1156
  helix:  1.34 (0.19), residues: 750
  sheet:  0.25 (0.86), residues: 36
  loop : -0.81 (0.35), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 536 
 TYR   0.011   0.001   TYR A 232 
 PHE   0.027   0.002   PHE B 388 
 TRP   0.016   0.001   TRP B 284 
 HIS   0.002   0.001   HIS B 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 9196)
  covalent geometry    : angle       0.57385 (12470)
  hydrogen bonds       : bond        0.04663 (  612)
  hydrogen bonds       : angle       4.28907 ( 1800)

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 0.216 
Fit side-chains
REVERT: B  225 ARG cc_start: 0.7998 (mtt90) cc_final: 0.7730 (mtt90)
REVERT: B  632 LEU cc_start: 0.7931 (mp) cc_final: 0.7639 (mp)
REVERT: A  225 ARG cc_start: 0.7922 (mtt90) cc_final: 0.7641 (mtt90)
REVERT: A  441 ILE cc_start: 0.8849 (mt) cc_final: 0.8422 (mm)
REVERT: A  595 ASP cc_start: 0.8129 (t0) cc_final: 0.7675 (p0)
REVERT: A  657 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7293 (pm20)
  outliers start: 21
  outliers final: 10
  residues processed: 106
  average time/residue: 0.3605
  time to fit residues: 42.2347
Evaluate side-chains
  103 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  293 ASN
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain A residue  602 ASP
Chi-restraints excluded: chain A residue  657 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 34 optimal weight:    9.9990
   chunk 55 optimal weight:   20.0000
   chunk 16 optimal weight:    0.3980
   chunk 26 optimal weight:    0.6980
   chunk 74 optimal weight:    0.3980
   chunk 58 optimal weight:    8.9990
   chunk 54 optimal weight:    5.9990
   chunk 103 optimal weight:    0.9980
   chunk 108 optimal weight:    7.9990
   chunk 53 optimal weight:    4.9990
   chunk 85 optimal weight:    1.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
B  99 GLN
** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 621 ASN
** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.207781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.119289 restraints weight = 9685.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 2.00
r_work: 0.3274 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3127 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9196  Z= 0.154
  Angle     :  0.570   7.417  12470  Z= 0.302
  Chirality :  0.042   0.152   1464
  Planarity :  0.003   0.034   1584
  Dihedral  :  4.487  18.605   1268
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 16.63 %
    Favored  : 80.87 %
  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 are not related in a simple way.
  whole:  1.23 (0.25), residues: 1156
  helix:  1.61 (0.19), residues: 740
  sheet:  0.24 (0.85), residues: 36
  loop : -0.68 (0.35), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 138 
 TYR   0.010   0.001   TYR A 232 
 PHE   0.026   0.002   PHE A 388 
 TRP   0.015   0.001   TRP B 284 
 HIS   0.002   0.001   HIS B 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 9196)
  covalent geometry    : angle       0.57019 (12470)
  hydrogen bonds       : bond        0.04631 (  612)
  hydrogen bonds       : angle       4.22688 ( 1800)

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 102
  time to evaluate  : 0.336 
Fit side-chains
REVERT: B  225 ARG cc_start: 0.7983 (mtt90) cc_final: 0.7724 (mtt90)
REVERT: B  355 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.8025 (t80)
REVERT: B  468 LYS cc_start: 0.7401 (mmmm) cc_final: 0.7059 (mmmm)
REVERT: B  515 LYS cc_start: 0.8433 (ttpt) cc_final: 0.8136 (ttmm)
REVERT: B  632 LEU cc_start: 0.7888 (mp) cc_final: 0.7633 (mp)
REVERT: A  355 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.8060 (t80)
REVERT: A  441 ILE cc_start: 0.8851 (mt) cc_final: 0.8431 (mm)
REVERT: A  595 ASP cc_start: 0.8187 (t0) cc_final: 0.7769 (p0)
REVERT: A  657 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7291 (pm20)
  outliers start: 24
  outliers final: 13
  residues processed: 116
  average time/residue: 0.3336
  time to fit residues: 42.8947
Evaluate side-chains
  110 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  301 THR
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  530 THR
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  293 ASN
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  602 ASP
Chi-restraints excluded: chain A residue  657 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 105 optimal weight:   10.0000
   chunk 57 optimal weight:    0.0980
   chunk 2 optimal weight:    0.5980
   chunk 58 optimal weight:    8.9990
   chunk 6 optimal weight:    0.0970
   chunk 17 optimal weight:    1.9990
   chunk 52 optimal weight:   20.0000
   chunk 92 optimal weight:   10.0000
   chunk 30 optimal weight:    0.3980
   chunk 66 optimal weight:    0.9980
   chunk 96 optimal weight:   10.0000
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 503 GLN
** A 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.209112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.124075 restraints weight = 9515.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 1.94
r_work: 0.3325 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3178 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.2381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9196  Z= 0.119
  Angle     :  0.537   7.586  12470  Z= 0.282
  Chirality :  0.041   0.172   1464
  Planarity :  0.003   0.030   1584
  Dihedral  :  4.273  17.837   1268
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 18.50 %
    Favored  : 79.31 %
  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 are not related in a simple way.
  whole:  1.54 (0.26), residues: 1156
  helix:  1.87 (0.19), residues: 742
  sheet:  0.39 (0.85), residues: 36
  loop : -0.61 (0.36), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 536 
 TYR   0.010   0.001   TYR A 232 
 PHE   0.023   0.002   PHE B 388 
 TRP   0.015   0.001   TRP B 284 
 HIS   0.003   0.001   HIS B 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 9196)
  covalent geometry    : angle       0.53707 (12470)
  hydrogen bonds       : bond        0.04220 (  612)
  hydrogen bonds       : angle       4.05340 ( 1800)

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 0.351 
Fit side-chains
REVERT: B  225 ARG cc_start: 0.7933 (mtt90) cc_final: 0.7650 (mtt90)
REVERT: B  331 GLN cc_start: 0.8010 (tt0) cc_final: 0.7522 (mt0)
REVERT: B  371 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7934 (mm)
REVERT: B  468 LYS cc_start: 0.7408 (mmmm) cc_final: 0.7047 (mmmm)
REVERT: B  515 LYS cc_start: 0.8476 (ttpt) cc_final: 0.8180 (ttmm)
REVERT: B  632 LEU cc_start: 0.8039 (mp) cc_final: 0.7747 (mp)
REVERT: A  221 ARG cc_start: 0.7678 (ttm110) cc_final: 0.7386 (ttm110)
REVERT: A  355 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.8041 (t80)
REVERT: A  371 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7913 (mm)
REVERT: A  595 ASP cc_start: 0.8146 (t0) cc_final: 0.7865 (p0)
REVERT: A  657 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7389 (pm20)
  outliers start: 21
  outliers final: 12
  residues processed: 118
  average time/residue: 0.3852
  time to fit residues: 49.9853
Evaluate side-chains
  109 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  293 ASN
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  602 ASP
Chi-restraints excluded: chain A residue  657 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 74 optimal weight:    0.0040
   chunk 83 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 66 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   chunk 73 optimal weight:    0.7980
   chunk 68 optimal weight:    3.9990
   chunk 24 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0060
   chunk 54 optimal weight:    8.9990
   chunk 3 optimal weight:    0.0470
   overall best weight:    0.3106

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

Flipped N/Q/H residues before XYZ refinement:
B 503 GLN
A 541 ASN
A 552 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.209923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.125155 restraints weight = 9522.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 1.95
r_work: 0.3346 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3199 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.2598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9196  Z= 0.114
  Angle     :  0.525   7.300  12470  Z= 0.277
  Chirality :  0.041   0.157   1464
  Planarity :  0.003   0.026   1584
  Dihedral  :  4.182  17.845   1268
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 19.85 %
    Favored  : 77.86 %
  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 are not related in a simple way.
  whole:  1.83 (0.26), residues: 1156
  helix:  2.09 (0.19), residues: 740
  sheet:  0.52 (0.87), residues: 36
  loop : -0.48 (0.36), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 536 
 TYR   0.010   0.001   TYR A 232 
 PHE   0.025   0.002   PHE A 210 
 TRP   0.014   0.001   TRP A 284 
 HIS   0.003   0.000   HIS B 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 9196)
  covalent geometry    : angle       0.52483 (12470)
  hydrogen bonds       : bond        0.04089 (  612)
  hydrogen bonds       : angle       3.96745 ( 1800)

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 100
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
REVERT: B  221 ARG cc_start: 0.7747 (ttm110) cc_final: 0.7380 (ttm110)
REVERT: B  225 ARG cc_start: 0.7928 (mtt90) cc_final: 0.7670 (mtt90)
REVERT: B  331 GLN cc_start: 0.7979 (tt0) cc_final: 0.7524 (mt0)
REVERT: B  371 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7884 (mm)
REVERT: B  468 LYS cc_start: 0.7427 (mmmm) cc_final: 0.7063 (mmmm)
REVERT: B  515 LYS cc_start: 0.8460 (ttpt) cc_final: 0.8167 (ttmm)
REVERT: B  632 LEU cc_start: 0.8029 (mp) cc_final: 0.7782 (mp)
REVERT: A  371 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7848 (mm)
REVERT: A  404 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7243 (mp)
REVERT: A  416 ASP cc_start: 0.7728 (m-30) cc_final: 0.7219 (p0)
REVERT: A  441 ILE cc_start: 0.8882 (mt) cc_final: 0.8282 (mm)
REVERT: A  515 LYS cc_start: 0.8434 (ttpt) cc_final: 0.8224 (ttmm)
REVERT: A  595 ASP cc_start: 0.8154 (t0) cc_final: 0.7899 (p0)
REVERT: A  657 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7378 (pm20)
  outliers start: 22
  outliers final: 13
  residues processed: 116
  average time/residue: 0.4157
  time to fit residues: 52.9201
Evaluate side-chains
  109 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  530 THR
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  293 ASN
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  602 ASP
Chi-restraints excluded: chain A residue  622 GLU
Chi-restraints excluded: chain A residue  657 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 64 optimal weight:    0.3980
   chunk 41 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 95 optimal weight:    0.0470
   chunk 83 optimal weight:    0.0980
   chunk 114 optimal weight:    9.9990
   chunk 47 optimal weight:    9.9990
   chunk 91 optimal weight:   10.0000
   chunk 42 optimal weight:    0.4980
   chunk 75 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.6080

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

Flipped N/Q/H residues before XYZ refinement:
A 541 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.210358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.123304 restraints weight = 9637.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 2.02
r_work: 0.3323 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3174 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.2642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9196  Z= 0.128
  Angle     :  0.541   7.505  12470  Z= 0.283
  Chirality :  0.041   0.149   1464
  Planarity :  0.003   0.031   1584
  Dihedral  :  4.170  16.747   1268
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 20.17 %
    Favored  : 77.75 %
  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 are not related in a simple way.
  whole:  1.80 (0.26), residues: 1156
  helix:  2.08 (0.19), residues: 742
  sheet:  0.49 (0.87), residues: 36
  loop : -0.53 (0.36), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 221 
 TYR   0.019   0.001   TYR A 537 
 PHE   0.022   0.002   PHE B 388 
 TRP   0.014   0.001   TRP B 284 
 HIS   0.003   0.000   HIS A 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 9196)
  covalent geometry    : angle       0.54078 (12470)
  hydrogen bonds       : bond        0.04232 (  612)
  hydrogen bonds       : angle       3.95243 ( 1800)

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
REVERT: B  221 ARG cc_start: 0.7708 (ttm110) cc_final: 0.7321 (ttm110)
REVERT: B  225 ARG cc_start: 0.7917 (mtt90) cc_final: 0.7649 (mtt90)
REVERT: B  331 GLN cc_start: 0.8010 (tt0) cc_final: 0.7534 (mt0)
REVERT: B  355 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.8025 (t80)
REVERT: B  371 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7929 (mm)
REVERT: B  468 LYS cc_start: 0.7436 (mmmm) cc_final: 0.7088 (mmmm)
REVERT: B  515 LYS cc_start: 0.8430 (ttpt) cc_final: 0.8148 (ttmm)
REVERT: B  632 LEU cc_start: 0.8017 (mp) cc_final: 0.7771 (mp)
REVERT: A  404 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7274 (mp)
REVERT: A  416 ASP cc_start: 0.7758 (m-30) cc_final: 0.7221 (p0)
REVERT: A  595 ASP cc_start: 0.8183 (t0) cc_final: 0.7944 (p0)
REVERT: A  657 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7359 (pm20)
  outliers start: 20
  outliers final: 13
  residues processed: 115
  average time/residue: 0.3503
  time to fit residues: 44.3814
Evaluate side-chains
  112 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 95
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  530 THR
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  293 ASN
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  602 ASP
Chi-restraints excluded: chain A residue  622 GLU
Chi-restraints excluded: chain A residue  657 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 111 optimal weight:    9.9990
   chunk 26 optimal weight:    0.5980
   chunk 36 optimal weight:    3.9990
   chunk 25 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 78 optimal weight:    3.9990
   chunk 115 optimal weight:    9.9990
   chunk 17 optimal weight:    1.9990
   chunk 113 optimal weight:    8.9990
   chunk 91 optimal weight:    9.9990
   chunk 87 optimal weight:    0.7980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 541 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.207851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.121560 restraints weight = 9502.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 1.96
r_work: 0.3285 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3138 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.2591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9196  Z= 0.161
  Angle     :  0.570   7.802  12470  Z= 0.298
  Chirality :  0.043   0.194   1464
  Planarity :  0.003   0.041   1584
  Dihedral  :  4.205  16.542   1268
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 20.69 %
    Favored  : 77.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.58 (0.26), residues: 1156
  helix:  1.86 (0.19), residues: 752
  sheet:  0.48 (0.87), residues: 36
  loop : -0.57 (0.36), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 221 
 TYR   0.019   0.001   TYR A 537 
 PHE   0.026   0.002   PHE A 210 
 TRP   0.013   0.001   TRP A 284 
 HIS   0.004   0.001   HIS A 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 9196)
  covalent geometry    : angle       0.56982 (12470)
  hydrogen bonds       : bond        0.04497 (  612)
  hydrogen bonds       : angle       4.00910 ( 1800)

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
REVERT: B  221 ARG cc_start: 0.7672 (ttm110) cc_final: 0.7442 (ttm110)
REVERT: B  225 ARG cc_start: 0.7884 (mtt90) cc_final: 0.7628 (mtt90)
REVERT: B  355 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.8025 (t80)
REVERT: B  468 LYS cc_start: 0.7414 (mmmm) cc_final: 0.7062 (mmmm)
REVERT: B  515 LYS cc_start: 0.8347 (ttpt) cc_final: 0.8080 (ttmm)
REVERT: B  632 LEU cc_start: 0.7952 (mp) cc_final: 0.7668 (mp)
REVERT: A  416 ASP cc_start: 0.7763 (m-30) cc_final: 0.7261 (p0)
REVERT: A  557 HIS cc_start: 0.7417 (t-90) cc_final: 0.7010 (m-70)
REVERT: A  657 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7328 (pm20)
  outliers start: 22
  outliers final: 14
  residues processed: 113
  average time/residue: 0.3748
  time to fit residues: 46.6797
Evaluate side-chains
  109 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  530 THR
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain A residue  100 MET
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  293 ASN
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  622 GLU
Chi-restraints excluded: chain A residue  657 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    2.9990
   chunk 106 optimal weight:    8.9990
   chunk 39 optimal weight:    5.9990
   chunk 88 optimal weight:    0.0980
   chunk 78 optimal weight:    3.9990
   chunk 92 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   chunk 93 optimal weight:   10.0000
   chunk 89 optimal weight:    0.9990
   chunk 103 optimal weight:    6.9990
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
B 621 ASN
A 541 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.209768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.122474 restraints weight = 9681.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 2.03
r_work: 0.3267 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3117 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.2712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9196  Z= 0.139
  Angle     :  0.578   8.317  12470  Z= 0.297
  Chirality :  0.043   0.204   1464
  Planarity :  0.003   0.036   1584
  Dihedral  :  4.159  16.499   1268
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 21.62 %
    Favored  : 76.92 %
  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 are not related in a simple way.
  whole:  1.71 (0.26), residues: 1156
  helix:  1.98 (0.19), residues: 742
  sheet:  0.49 (0.87), residues: 36
  loop : -0.48 (0.36), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 221 
 TYR   0.018   0.001   TYR A 537 
 PHE   0.023   0.002   PHE B 388 
 TRP   0.013   0.001   TRP B 284 
 HIS   0.003   0.000   HIS A 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 9196)
  covalent geometry    : angle       0.57836 (12470)
  hydrogen bonds       : bond        0.04344 (  612)
  hydrogen bonds       : angle       3.97248 ( 1800)

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
REVERT: B  221 ARG cc_start: 0.7625 (ttm110) cc_final: 0.7387 (ttm110)
REVERT: B  225 ARG cc_start: 0.7777 (mtt90) cc_final: 0.7501 (mtt90)
REVERT: B  331 GLN cc_start: 0.7883 (tt0) cc_final: 0.7581 (mt0)
REVERT: B  355 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.8001 (t80)
REVERT: B  468 LYS cc_start: 0.7377 (mmmm) cc_final: 0.7030 (mmmm)
REVERT: B  515 LYS cc_start: 0.8288 (ttpt) cc_final: 0.8035 (ttmm)
REVERT: B  632 LEU cc_start: 0.7876 (mp) cc_final: 0.7639 (mp)
REVERT: A  355 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.7976 (t80)
REVERT: A  416 ASP cc_start: 0.7727 (m-30) cc_final: 0.7163 (p0)
REVERT: A  441 ILE cc_start: 0.8586 (mt) cc_final: 0.8055 (mm)
REVERT: A  557 HIS cc_start: 0.7428 (t-90) cc_final: 0.7018 (m-70)
REVERT: A  657 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7321 (pm20)
  outliers start: 14
  outliers final: 13
  residues processed: 108
  average time/residue: 0.4110
  time to fit residues: 48.7335
Evaluate side-chains
  110 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  530 THR
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  293 ASN
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  622 GLU
Chi-restraints excluded: chain A residue  657 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 96 optimal weight:    8.9990
   chunk 57 optimal weight:    7.9990
   chunk 91 optimal weight:    1.9990
   chunk 110 optimal weight:    7.9990
   chunk 31 optimal weight:    1.9990
   chunk 98 optimal weight:    7.9990
   chunk 108 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 29 optimal weight:    0.6980
   chunk 90 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
B 621 ASN
A 541 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.205876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.117005 restraints weight = 9654.107|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 2.01
r_work: 0.3193 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3045 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.2545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059   9196  Z= 0.227
  Angle     :  0.627   7.884  12470  Z= 0.326
  Chirality :  0.046   0.191   1464
  Planarity :  0.004   0.055   1584
  Dihedral  :  4.305  16.320   1268
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 21.83 %
    Favored  : 76.40 %
  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 are not related in a simple way.
  whole:  1.38 (0.25), residues: 1156
  helix:  1.62 (0.18), residues: 750
  sheet:  0.69 (0.84), residues: 38
  loop : -0.48 (0.36), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 221 
 TYR   0.022   0.001   TYR A 537 
 PHE   0.024   0.002   PHE A 388 
 TRP   0.012   0.002   TRP A 284 
 HIS   0.004   0.001   HIS A 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00552 ( 9196)
  covalent geometry    : angle       0.62742 (12470)
  hydrogen bonds       : bond        0.04969 (  612)
  hydrogen bonds       : angle       4.16468 ( 1800)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3514.98 seconds
wall clock time: 60 minutes 26.39 seconds (3626.39 seconds total)