Starting phenix.real_space_refine
on Wed Sep 17 12:29:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vpa_43405/09_2025/8vpa_43405.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vpa_43405/09_2025/8vpa_43405.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.11
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vpa_43405/09_2025/8vpa_43405.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vpa_43405/09_2025/8vpa_43405.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vpa_43405/09_2025/8vpa_43405.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vpa_43405/09_2025/8vpa_43405.cif"
  }
  resolution = 3.11
  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=   0.002 sd=   0.021
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      42      5.16       5
     C    5618      2.51       5
     N    1404      2.21       5
     O    1590      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8658
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4302
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 549, 4302
          Classifications: {'peptide': 549}
          Link IDs: {'PTRANS': 10, 'TRANS': 538}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 4302
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 549, 4302
          Classifications: {'peptide': 549}
          Link IDs: {'PTRANS': 10, 'TRANS': 538}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.32, per 1000 atoms: 0.27
  Number of scatterers: 8658
  At special positions: 0
  Unit cell: (69.229, 95.756, 137.164, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      42     16.00
     P       4     15.00
     O    1590      8.00
     N    1404      7.00
     C    5618      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: 0.88
  Conformation dependent library (CDL) restraints added in 359.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2048

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 6 sheets defined
      71.5% alpha, 8.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 153 through 163
    Processing helix  chain 'A' and resid 167 through 193
      removed outlier: 3.790A  pdb=" N   SER A 187 " --> pdb=" O   GLY A 183 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   PHE A 188 " --> pdb=" O   ILE A 184 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   TYR A 189 " --> pdb=" O   ALA A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 201
      removed outlier: 3.591A  pdb=" N   PHE A 200 " --> pdb=" O   ASP A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 251
    Processing helix  chain 'A' and resid 254 through 261
      removed outlier: 3.917A  pdb=" N   PHE A 258 " --> pdb=" O   PRO A 254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 272
    Processing helix  chain 'A' and resid 272 through 280
      removed outlier: 4.167A  pdb=" N   ILE A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 305
      removed outlier: 3.875A  pdb=" N   MET A 288 " --> pdb=" O   THR A 284 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ILE A 289 " --> pdb=" O   LEU A 285 " (cutoff:3.500A)
      removed outlier: 4.669A  pdb=" N   VAL A 295 " --> pdb=" O   THR A 291 " (cutoff:3.500A)
      removed outlier: 5.845A  pdb=" N   ILE A 296 " --> pdb=" O   ILE A 292 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   GLY A 297 " --> pdb=" O   MET A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 354
      removed outlier: 3.559A  pdb=" N   PHE A 326 " --> pdb=" O   ILE A 322 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ASN A 327 " --> pdb=" O   VAL A 323 " (cutoff:3.500A)
      removed outlier: 4.840A  pdb=" N   LYS A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
      Proline residue:  A 329  - end of helix
    Processing helix  chain 'A' and resid 354 through 362
    Processing helix  chain 'A' and resid 363 through 417
      removed outlier: 3.573A  pdb=" N   LYS A 374 " --> pdb=" O   SER A 370 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   THR A 377 " --> pdb=" O   ASP A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 432
    Processing helix  chain 'A' and resid 433 through 435
      No H-bonds generated for 'chain 'A' and resid 433 through 435'
    Processing helix  chain 'A' and resid 436 through 445
    Processing helix  chain 'A' and resid 445 through 464
      removed outlier: 3.621A  pdb=" N   ILE A 462 " --> pdb=" O   ARG A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 472
      removed outlier: 3.556A  pdb=" N   ARG A 472 " --> pdb=" O   LYS A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 533
    Processing helix  chain 'A' and resid 549 through 553
      removed outlier: 3.593A  pdb=" N   ILE A 553 " --> pdb=" O   ILE A 550 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 554 through 561
    Processing helix  chain 'A' and resid 576 through 581
    Processing helix  chain 'A' and resid 588 through 599
    Processing helix  chain 'A' and resid 601 through 607
    Processing helix  chain 'A' and resid 617 through 621
    Processing helix  chain 'A' and resid 624 through 638
      removed outlier: 3.702A  pdb=" N   ARG A 630 " --> pdb=" O   GLY A 626 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 684
      removed outlier: 3.658A  pdb=" N   THR A 683 " --> pdb=" O   ARG A 680 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   ILE A 684 " --> pdb=" O   LEU A 681 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 680 through 684'
    Processing helix  chain 'A' and resid 703 through 711
      removed outlier: 3.573A  pdb=" N   LYS A 711 " --> pdb=" O   LEU A 707 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 712 through 721
    Processing helix  chain 'B' and resid 154 through 162
    Processing helix  chain 'B' and resid 166 through 187
    Processing helix  chain 'B' and resid 188 through 196
      removed outlier: 3.570A  pdb=" N   ASP B 196 " --> pdb=" O   PHE B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 201
      removed outlier: 3.647A  pdb=" N   PHE B 200 " --> pdb=" O   ASP B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 251
      removed outlier: 3.501A  pdb=" N   LEU B 218 " --> pdb=" O   ALA B 214 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LEU B 219 " --> pdb=" O   VAL B 215 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   GLN B 220 " --> pdb=" O   ILE B 216 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 261
      removed outlier: 3.841A  pdb=" N   PHE B 258 " --> pdb=" O   PRO B 254 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 262 through 272
    Processing helix  chain 'B' and resid 272 through 280
      removed outlier: 4.061A  pdb=" N   ILE B 276 " --> pdb=" O   ASP B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 305
      removed outlier: 3.693A  pdb=" N   MET B 288 " --> pdb=" O   THR B 284 " (cutoff:3.500A)
      removed outlier: 4.861A  pdb=" N   VAL B 295 " --> pdb=" O   THR B 291 " (cutoff:3.500A)
      removed outlier: 5.742A  pdb=" N   ILE B 296 " --> pdb=" O   ILE B 292 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   GLY B 297 " --> pdb=" O   MET B 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 305 through 354
      removed outlier: 4.853A  pdb=" N   LYS B 328 " --> pdb=" O   THR B 324 " (cutoff:3.500A)
      Proline residue:  B 329  - end of helix
    Processing helix  chain 'B' and resid 354 through 362
    Processing helix  chain 'B' and resid 363 through 418
    Processing helix  chain 'B' and resid 421 through 432
    Processing helix  chain 'B' and resid 435 through 445
      removed outlier: 4.350A  pdb=" N   VAL B 439 " --> pdb=" O   PHE B 435 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 445 through 464
    Processing helix  chain 'B' and resid 524 through 533
    Processing helix  chain 'B' and resid 551 through 553
      No H-bonds generated for 'chain 'B' and resid 551 through 553'
    Processing helix  chain 'B' and resid 554 through 561
    Processing helix  chain 'B' and resid 576 through 581
    Processing helix  chain 'B' and resid 590 through 599
    Processing helix  chain 'B' and resid 601 through 607
    Processing helix  chain 'B' and resid 617 through 621
    Processing helix  chain 'B' and resid 624 through 638
    Processing helix  chain 'B' and resid 703 through 710
    Processing helix  chain 'B' and resid 712 through 722
    Processing sheet with id=AA1, first strand: chain 'A' and resid 502 through 509
      removed outlier: 6.939A  pdb=" N   LYS A 503 " --> pdb=" O   ASP A 492 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   ASP A 492 " --> pdb=" O   LYS A 503 " (cutoff:3.500A)
      removed outlier: 5.119A  pdb=" N   ILE A 505 " --> pdb=" O   ASN A 490 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 562 through 565
      removed outlier: 6.422A  pdb=" N   ALA A 563 " --> pdb=" O   ILE A 645 " (cutoff:3.500A)
      removed outlier: 7.989A  pdb=" N   ASP A 647 " --> pdb=" O   ALA A 563 " (cutoff:3.500A)
      removed outlier: 7.265A  pdb=" N   VAL A 565 " --> pdb=" O   ASP A 647 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   LEU A 644 " --> pdb=" O   ILE A 675 " (cutoff:3.500A)
      removed outlier: 7.496A  pdb=" N   ILE A 677 " --> pdb=" O   LEU A 644 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   LEU A 646 " --> pdb=" O   ILE A 677 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   THR A 514 " --> pdb=" O   LYS A 689 " (cutoff:3.500A)
      removed outlier: 8.512A  pdb=" N   TYR A 691 " --> pdb=" O   THR A 514 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   ALA A 516 " --> pdb=" O   TYR A 691 " (cutoff:3.500A)
      removed outlier: 7.587A  pdb=" N   LEU A 693 " --> pdb=" O   ALA A 516 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   VAL A 518 " --> pdb=" O   LEU A 693 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   GLU A 700 " --> pdb=" O   LEU A 692 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   LYS A 694 " --> pdb=" O   ILE A 698 " (cutoff:3.500A)
      removed outlier: 4.978A  pdb=" N   ILE A 698 " --> pdb=" O   LYS A 694 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 574 through 575
    Processing sheet with id=AA4, first strand: chain 'B' and resid 502 through 509
      removed outlier: 7.202A  pdb=" N   LYS B 503 " --> pdb=" O   ASP B 492 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   ASP B 492 " --> pdb=" O   LYS B 503 " (cutoff:3.500A)
      removed outlier: 5.581A  pdb=" N   ILE B 505 " --> pdb=" O   ASN B 490 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ASN B 490 " --> pdb=" O   ILE B 505 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   VAL B 491 " --> pdb=" O   LYS B 540 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   LYS B 540 " --> pdb=" O   VAL B 491 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 562 through 565
      removed outlier: 6.374A  pdb=" N   ALA B 563 " --> pdb=" O   ILE B 645 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   LEU B 644 " --> pdb=" O   ILE B 675 " (cutoff:3.500A)
      removed outlier: 7.394A  pdb=" N   ILE B 677 " --> pdb=" O   LEU B 644 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   LEU B 646 " --> pdb=" O   ILE B 677 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   THR B 514 " --> pdb=" O   LYS B 689 " (cutoff:3.500A)
      removed outlier: 8.492A  pdb=" N   TYR B 691 " --> pdb=" O   THR B 514 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   ALA B 516 " --> pdb=" O   TYR B 691 " (cutoff:3.500A)
      removed outlier: 7.602A  pdb=" N   LEU B 693 " --> pdb=" O   ALA B 516 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   VAL B 518 " --> pdb=" O   LEU B 693 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   GLU B 700 " --> pdb=" O   LEU B 692 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   LYS B 694 " --> pdb=" O   ILE B 698 " (cutoff:3.500A)
      removed outlier: 4.955A  pdb=" N   ILE B 698 " --> pdb=" O   LYS B 694 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 574 through 575

    577 hydrogen bonds defined for protein.
    1695 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: 1.53

  Time building geometry restraints manager: 1.07 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2705
        1.34 -     1.46: 1614
        1.46 -     1.58: 4391
        1.58 -     1.69: 6
        1.69 -     1.81: 76
  Bond restraints: 8792
  Sorted by residual:
  bond pdb=" C4  ADP A 801 "
       pdb=" C5  ADP A 801 "
    ideal  model  delta    sigma   weight residual
    1.490  1.469  0.021 2.00e-02 2.50e+03 1.14e+00
  bond pdb=" C   GLY A 186 "
       pdb=" O   GLY A 186 "
    ideal  model  delta    sigma   weight residual
    1.234  1.248 -0.014 1.29e-02 6.01e+03 1.13e+00
  bond pdb=" C4  ADP B 801 "
       pdb=" C5  ADP B 801 "
    ideal  model  delta    sigma   weight residual
    1.490  1.469  0.021 2.00e-02 2.50e+03 1.12e+00
  bond pdb=" N   GLY A 186 "
       pdb=" CA  GLY A 186 "
    ideal  model  delta    sigma   weight residual
    1.452  1.466 -0.014 1.34e-02 5.57e+03 1.02e+00
  bond pdb=" C   LEU B 253 "
       pdb=" N   PRO B 254 "
    ideal  model  delta    sigma   weight residual
    1.331  1.343 -0.011 1.21e-02 6.83e+03 8.98e-01
  ... (remaining 8787 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.80: 11703
        1.80 -     3.60: 105
        3.60 -     5.40: 37
        5.40 -     7.20: 6
        7.20 -     9.00: 1
  Bond angle restraints: 11852
  Sorted by residual:
  angle pdb=" C   LYS A 611 "
        pdb=" CA  LYS A 611 "
        pdb=" CB  LYS A 611 "
      ideal   model   delta    sigma   weight residual
     116.54  110.32    6.22 1.15e+00 7.56e-01 2.92e+01
  angle pdb=" CG1 ILE B 280 "
        pdb=" CB  ILE B 280 "
        pdb=" CG2 ILE B 280 "
      ideal   model   delta    sigma   weight residual
     110.70  101.70    9.00 3.00e+00 1.11e-01 8.99e+00
  angle pdb=" C   GLU B 585 "
        pdb=" N   ASN B 586 "
        pdb=" CA  ASN B 586 "
      ideal   model   delta    sigma   weight residual
     122.07  125.68   -3.61 1.43e+00 4.89e-01 6.38e+00
  angle pdb=" CA  LYS A 611 "
        pdb=" C   LYS A 611 "
        pdb=" N   TYR A 612 "
      ideal   model   delta    sigma   weight residual
     119.52  117.53    1.99 7.90e-01 1.60e+00 6.37e+00
  angle pdb=" N   LYS A 611 "
        pdb=" CA  LYS A 611 "
        pdb=" C   LYS A 611 "
      ideal   model   delta    sigma   weight residual
     108.31  111.94   -3.63 1.52e+00 4.33e-01 5.71e+00
  ... (remaining 11847 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.40: 4752
       17.40 -    34.79: 455
       34.79 -    52.19: 91
       52.19 -    69.59: 18
       69.59 -    86.99: 6
  Dihedral angle restraints: 5322
    sinusoidal: 2148
      harmonic: 3174
  Sorted by residual:
  dihedral pdb=" C5' ADP B 801 "
           pdb=" O5' ADP B 801 "
           pdb=" PA  ADP B 801 "
           pdb=" O2A ADP B 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -137.22   77.22     1      2.00e+01 2.50e-03 1.87e+01
  dihedral pdb=" C5' ADP A 801 "
           pdb=" O5' ADP A 801 "
           pdb=" PA  ADP A 801 "
           pdb=" O2A ADP A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -127.04   67.04     1      2.00e+01 2.50e-03 1.46e+01
  dihedral pdb=" CG  ARG A 458 "
           pdb=" CD  ARG A 458 "
           pdb=" NE  ARG A 458 "
           pdb=" CZ  ARG A 458 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -133.80   43.80     2      1.50e+01 4.44e-03 1.02e+01
  ... (remaining 5319 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1113
       0.046 -    0.092: 250
       0.092 -    0.138: 50
       0.138 -    0.184: 0
       0.184 -    0.231: 1
  Chirality restraints: 1414
  Sorted by residual:
  chirality pdb=" CB  ILE B 280 "
            pdb=" CA  ILE B 280 "
            pdb=" CG1 ILE B 280 "
            pdb=" CG2 ILE B 280 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.88   -0.23 2.00e-01 2.50e+01 1.33e+00
  chirality pdb=" CA  ILE B 543 "
            pdb=" N   ILE B 543 "
            pdb=" C   ILE B 543 "
            pdb=" CB  ILE B 543 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.64e-01
  chirality pdb=" CB  ILE B 480 "
            pdb=" CA  ILE B 480 "
            pdb=" CG1 ILE B 480 "
            pdb=" CG2 ILE B 480 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.13 2.00e-01 2.50e+01 4.26e-01
  ... (remaining 1411 not shown)

  Planarity restraints: 1454
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 328 "    0.021 5.00e-02 4.00e+02   3.11e-02 1.55e+00
        pdb=" N   PRO A 329 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO A 329 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 329 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 446 "    0.019 5.00e-02 4.00e+02   2.87e-02 1.31e+00
        pdb=" N   PRO A 447 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO A 447 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 447 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B 446 "   -0.015 5.00e-02 4.00e+02   2.24e-02 8.00e-01
        pdb=" N   PRO B 447 "    0.039 5.00e-02 4.00e+02
        pdb=" CA  PRO B 447 "   -0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO B 447 "   -0.013 5.00e-02 4.00e+02
  ... (remaining 1451 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1372
        2.76 -     3.29: 8525
        3.29 -     3.83: 14348
        3.83 -     4.36: 16626
        4.36 -     4.90: 29921
  Nonbonded interactions: 70792
  Sorted by model distance:
  nonbonded pdb=" O   THR B 508 "
            pdb=" OH  TYR B 691 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" O   LEU B 610 "
            pdb=" OG1 THR B 614 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" O   THR A 508 "
            pdb=" OH  TYR A 691 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" ND1 HIS A 602 "
            pdb=" OH  TYR A 612 "
     model   vdw
     2.297 3.120
  nonbonded pdb=" OD1 ASN A 224 "
            pdb=" NH2 ARG A 227 "
     model   vdw
     2.329 3.120
  ... (remaining 70787 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:             4.080
  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:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     9.880
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
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      :  0.003   0.033   8792  Z= 0.125
  Angle     :  0.521   8.996  11852  Z= 0.269
  Chirality :  0.039   0.231   1414
  Planarity :  0.002   0.031   1454
  Dihedral  : 14.438  86.985   3274
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.35 (0.27), residues: 1090
  helix:  2.42 (0.19), residues: 734
  sheet:  1.44 (0.71), residues: 70
  loop : -0.77 (0.38), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 277 
 TYR   0.011   0.001   TYR B 225 
 PHE   0.011   0.001   PHE A 217 
 TRP   0.002   0.001   TRP B 409 
 HIS   0.004   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 8792)
  covalent geometry    : angle       0.52108 (11852)
  hydrogen bonds       : bond        0.12931 (  577)
  hydrogen bonds       : angle       4.73747 ( 1695)

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.340 
Fit side-chains
REVERT: A  457 ASN cc_start: 0.8491 (m-40) cc_final: 0.8135 (m110)
REVERT: B  420 MET cc_start: 0.7975 (ttm) cc_final: 0.7748 (ttm)
REVERT: B  485 ASP cc_start: 0.7504 (m-30) cc_final: 0.7223 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.0904
  time to fit residues: 16.5298
Evaluate side-chains
  111 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    8.9990
   chunk 53 optimal weight:    0.0870
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    4.9990
   chunk 106 optimal weight:    6.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    1.0762

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

Flipped N/Q/H residues before XYZ refinement:
A 259 ASN
A 622 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.140233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.111384 restraints weight = 10077.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.3148 rms_B_bonded: 1.75
r_work: 0.3039 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2905 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.0673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8792  Z= 0.146
  Angle     :  0.522   6.187  11852  Z= 0.262
  Chirality :  0.041   0.200   1414
  Planarity :  0.003   0.031   1454
  Dihedral  :  5.340  75.727   1178
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  6.20 %
    Favored  : 92.86 %
  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 aren not related in a simple way.
  whole:  2.28 (0.27), residues: 1090
  helix:  2.39 (0.19), residues: 738
  sheet:  1.07 (0.68), residues: 70
  loop : -0.82 (0.38), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 277 
 TYR   0.011   0.001   TYR B 225 
 PHE   0.017   0.001   PHE A 604 
 TRP   0.003   0.001   TRP A 718 
 HIS   0.003   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 8792)
  covalent geometry    : angle       0.52248 (11852)
  hydrogen bonds       : bond        0.05187 (  577)
  hydrogen bonds       : angle       3.98565 ( 1695)

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 118
  time to evaluate  : 0.341 
Fit side-chains
REVERT: A  155 MET cc_start: 0.6154 (OUTLIER) cc_final: 0.5397 (mtm)
REVERT: A  158 PHE cc_start: 0.6393 (m-80) cc_final: 0.6193 (m-80)
REVERT: A  457 ASN cc_start: 0.8559 (m-40) cc_final: 0.8134 (m110)
REVERT: B  208 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7491 (mt)
REVERT: B  244 MET cc_start: 0.8119 (mmm) cc_final: 0.7891 (mmm)
REVERT: B  589 MET cc_start: 0.8783 (tpp) cc_final: 0.8509 (tpp)
REVERT: B  603 ASP cc_start: 0.8369 (m-30) cc_final: 0.8148 (m-30)
REVERT: B  622 ASN cc_start: 0.8541 (t0) cc_final: 0.8274 (t0)
  outliers start: 9
  outliers final: 7
  residues processed: 124
  average time/residue: 0.0926
  time to fit residues: 16.4705
Evaluate side-chains
  122 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 113
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 MET
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  480 ILE
Chi-restraints excluded: chain A residue  614 THR
Chi-restraints excluded: chain A residue  622 ASN
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  456 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 39 optimal weight:    5.9990
   chunk 100 optimal weight:    5.9990
   chunk 27 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 71 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 52 optimal weight:    7.9990
   chunk 69 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 622 ASN
B 586 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.138715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.109982 restraints weight = 9955.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 1.72
r_work: 0.3046 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2913 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.0843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8792  Z= 0.141
  Angle     :  0.506   6.065  11852  Z= 0.253
  Chirality :  0.040   0.195   1414
  Planarity :  0.003   0.029   1454
  Dihedral  :  5.288  71.998   1178
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  :  7.56 %
    Favored  : 91.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.33 (0.27), residues: 1090
  helix:  2.52 (0.19), residues: 734
  sheet:  0.95 (0.66), residues: 70
  loop : -1.00 (0.38), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 277 
 TYR   0.011   0.001   TYR A 226 
 PHE   0.013   0.001   PHE A 604 
 TRP   0.002   0.001   TRP B 409 
 HIS   0.003   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 8792)
  covalent geometry    : angle       0.50556 (11852)
  hydrogen bonds       : bond        0.04999 (  577)
  hydrogen bonds       : angle       3.85345 ( 1695)

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 121
  time to evaluate  : 0.336 
Fit side-chains
REVERT: A  158 PHE cc_start: 0.6422 (m-80) cc_final: 0.6193 (m-80)
REVERT: A  248 SER cc_start: 0.8247 (m) cc_final: 0.7958 (m)
REVERT: A  457 ASN cc_start: 0.8541 (m-40) cc_final: 0.8092 (m110)
REVERT: B  166 LYS cc_start: 0.7207 (tttm) cc_final: 0.6740 (mtpp)
REVERT: B  208 ILE cc_start: 0.7865 (OUTLIER) cc_final: 0.7478 (mt)
REVERT: B  244 MET cc_start: 0.8129 (mmm) cc_final: 0.7901 (mmm)
REVERT: B  589 MET cc_start: 0.8767 (tpp) cc_final: 0.8510 (tpp)
REVERT: B  603 ASP cc_start: 0.8364 (m-30) cc_final: 0.8142 (m-30)
  outliers start: 13
  outliers final: 8
  residues processed: 131
  average time/residue: 0.1027
  time to fit residues: 18.6095
Evaluate side-chains
  127 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 118
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  480 ILE
Chi-restraints excluded: chain A residue  622 ASN
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  248 SER
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  456 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 101 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 41 optimal weight:    0.3980
   chunk 105 optimal weight:    8.9990
   chunk 102 optimal weight:    0.9990
   chunk 73 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 32 optimal weight:    8.9990
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 622 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.141779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.113211 restraints weight = 10203.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 1.75
r_work: 0.3058 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2925 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.0944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8792  Z= 0.124
  Angle     :  0.489   5.992  11852  Z= 0.244
  Chirality :  0.040   0.204   1414
  Planarity :  0.002   0.028   1454
  Dihedral  :  5.224  68.274   1178
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  :  9.56 %
    Favored  : 89.18 %
  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:  2.42 (0.26), residues: 1090
  helix:  2.64 (0.19), residues: 732
  sheet:  0.91 (0.65), residues: 70
  loop : -1.07 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 472 
 TYR   0.010   0.001   TYR A 226 
 PHE   0.011   0.001   PHE A 217 
 TRP   0.002   0.001   TRP B 409 
 HIS   0.003   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 8792)
  covalent geometry    : angle       0.48897 (11852)
  hydrogen bonds       : bond        0.04730 (  577)
  hydrogen bonds       : angle       3.74484 ( 1695)

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 0.366 
Fit side-chains
REVERT: A  158 PHE cc_start: 0.6429 (m-80) cc_final: 0.6225 (m-80)
REVERT: A  248 SER cc_start: 0.8209 (m) cc_final: 0.7913 (m)
REVERT: A  457 ASN cc_start: 0.8544 (m-40) cc_final: 0.8128 (m-40)
REVERT: A  584 ASN cc_start: 0.7058 (t0) cc_final: 0.6750 (t0)
REVERT: B  166 LYS cc_start: 0.7165 (tttm) cc_final: 0.6703 (mtpp)
REVERT: B  208 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7465 (mt)
REVERT: B  244 MET cc_start: 0.8110 (mmm) cc_final: 0.7878 (mmm)
REVERT: B  494 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8542 (ptp-110)
REVERT: B  589 MET cc_start: 0.8753 (tpp) cc_final: 0.8488 (tpp)
REVERT: B  603 ASP cc_start: 0.8372 (m-30) cc_final: 0.8157 (m-30)
REVERT: B  604 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.8015 (p90)
  outliers start: 12
  outliers final: 8
  residues processed: 125
  average time/residue: 0.1027
  time to fit residues: 17.8009
Evaluate side-chains
  127 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 116
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  196 ASP
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  248 SER
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  456 SER
Chi-restraints excluded: chain B residue  494 ARG
Chi-restraints excluded: chain B residue  604 PHE
Chi-restraints excluded: chain B residue  710 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 13 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9980
   chunk 17 optimal weight:    0.4980
   chunk 83 optimal weight:    0.4980
   chunk 66 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 622 ASN
** B 567 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 = 0.3563 r_free = 0.3563 target = 0.142011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.113694 restraints weight = 9998.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 1.73
r_work: 0.3049 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2916 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.1064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8792  Z= 0.134
  Angle     :  0.498   6.070  11852  Z= 0.248
  Chirality :  0.040   0.203   1414
  Planarity :  0.003   0.029   1454
  Dihedral  :  5.213  65.545   1178
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  :  9.66 %
    Favored  : 88.24 %
  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:  2.39 (0.26), residues: 1090
  helix:  2.63 (0.19), residues: 734
  sheet:  0.83 (0.64), residues: 70
  loop : -1.11 (0.37), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 269 
 TYR   0.011   0.001   TYR A 226 
 PHE   0.012   0.001   PHE A 604 
 TRP   0.002   0.001   TRP B 409 
 HIS   0.003   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 8792)
  covalent geometry    : angle       0.49786 (11852)
  hydrogen bonds       : bond        0.04803 (  577)
  hydrogen bonds       : angle       3.70029 ( 1695)

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 0.368 
Fit side-chains
REVERT: A  248 SER cc_start: 0.8223 (m) cc_final: 0.7928 (m)
REVERT: A  457 ASN cc_start: 0.8514 (m-40) cc_final: 0.8090 (m-40)
REVERT: A  584 ASN cc_start: 0.7025 (t0) cc_final: 0.6721 (t0)
REVERT: B  166 LYS cc_start: 0.7148 (tttm) cc_final: 0.6692 (mtpp)
REVERT: B  208 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7460 (mt)
REVERT: B  244 MET cc_start: 0.8140 (mmm) cc_final: 0.7882 (mmm)
REVERT: B  589 MET cc_start: 0.8749 (tpp) cc_final: 0.8475 (tpp)
REVERT: B  603 ASP cc_start: 0.8399 (m-30) cc_final: 0.8186 (m-30)
REVERT: B  604 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.8154 (p90)
  outliers start: 20
  outliers final: 14
  residues processed: 129
  average time/residue: 0.0984
  time to fit residues: 17.6670
Evaluate side-chains
  127 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  196 ASP
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  480 ILE
Chi-restraints excluded: chain A residue  614 THR
Chi-restraints excluded: chain A residue  622 ASN
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  248 SER
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  456 SER
Chi-restraints excluded: chain B residue  503 LYS
Chi-restraints excluded: chain B residue  604 PHE
Chi-restraints excluded: chain B residue  710 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 42 optimal weight:    0.7980
   chunk 97 optimal weight:    2.9990
   chunk 51 optimal weight:    7.9990
   chunk 32 optimal weight:    9.9990
   chunk 107 optimal weight:    0.9980
   chunk 60 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 87 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9980
   chunk 106 optimal weight:    5.9990
   chunk 86 optimal weight:    5.9990
   overall best weight:    1.3382

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

Flipped N/Q/H residues before XYZ refinement:
A 622 ASN
B 567 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.141057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.112928 restraints weight = 10124.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.3129 rms_B_bonded: 1.69
r_work: 0.3021 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2888 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.1144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8792  Z= 0.159
  Angle     :  0.520   8.498  11852  Z= 0.260
  Chirality :  0.041   0.226   1414
  Planarity :  0.003   0.029   1454
  Dihedral  :  5.271  67.515   1178
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 10.82 %
    Favored  : 87.18 %
  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:  2.29 (0.26), residues: 1090
  helix:  2.55 (0.19), residues: 734
  sheet:  0.80 (0.64), residues: 70
  loop : -1.17 (0.37), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 269 
 TYR   0.011   0.001   TYR A 226 
 PHE   0.015   0.001   PHE A 604 
 TRP   0.003   0.001   TRP B 409 
 HIS   0.003   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 8792)
  covalent geometry    : angle       0.51974 (11852)
  hydrogen bonds       : bond        0.05048 (  577)
  hydrogen bonds       : angle       3.75006 ( 1695)

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.311 
Fit side-chains
REVERT: A  248 SER cc_start: 0.8281 (m) cc_final: 0.7984 (m)
REVERT: A  457 ASN cc_start: 0.8529 (m-40) cc_final: 0.8092 (m-40)
REVERT: A  584 ASN cc_start: 0.7070 (t0) cc_final: 0.6807 (t0)
REVERT: B  166 LYS cc_start: 0.7198 (tttm) cc_final: 0.6744 (mtpp)
REVERT: B  208 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7467 (mt)
REVERT: B  244 MET cc_start: 0.8228 (mmm) cc_final: 0.7897 (mmm)
REVERT: B  603 ASP cc_start: 0.8410 (m-30) cc_final: 0.8199 (m-30)
REVERT: B  604 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.8189 (p90)
  outliers start: 19
  outliers final: 14
  residues processed: 124
  average time/residue: 0.0978
  time to fit residues: 16.7388
Evaluate side-chains
  128 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 112
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  196 ASP
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  480 ILE
Chi-restraints excluded: chain A residue  614 THR
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  248 SER
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  337 ILE
Chi-restraints excluded: chain B residue  456 SER
Chi-restraints excluded: chain B residue  503 LYS
Chi-restraints excluded: chain B residue  604 PHE
Chi-restraints excluded: chain B residue  710 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 86 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 104 optimal weight:    0.9990
   chunk 73 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   chunk 91 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 622 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.140070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.111711 restraints weight = 10218.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3159 rms_B_bonded: 1.74
r_work: 0.3052 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2919 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.1168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8792  Z= 0.128
  Angle     :  0.495   8.289  11852  Z= 0.247
  Chirality :  0.040   0.214   1414
  Planarity :  0.002   0.029   1454
  Dihedral  :  5.217  64.073   1178
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 11.13 %
    Favored  : 86.97 %
  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:  2.24 (0.26), residues: 1090
  helix:  2.51 (0.19), residues: 746
  sheet:  1.29 (0.77), residues: 50
  loop : -1.33 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 494 
 TYR   0.010   0.001   TYR A 225 
 PHE   0.011   0.001   PHE A 217 
 TRP   0.003   0.001   TRP A 409 
 HIS   0.002   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 8792)
  covalent geometry    : angle       0.49462 (11852)
  hydrogen bonds       : bond        0.04716 (  577)
  hydrogen bonds       : angle       3.66395 ( 1695)

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 0.369 
Fit side-chains
REVERT: A  248 SER cc_start: 0.8219 (m) cc_final: 0.7925 (m)
REVERT: A  457 ASN cc_start: 0.8541 (m-40) cc_final: 0.8237 (m110)
REVERT: A  584 ASN cc_start: 0.7038 (t0) cc_final: 0.6794 (t0)
REVERT: B  166 LYS cc_start: 0.7140 (tttm) cc_final: 0.6676 (mtpp)
REVERT: B  208 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7457 (mt)
REVERT: B  244 MET cc_start: 0.8196 (mmm) cc_final: 0.7881 (mmm)
REVERT: B  603 ASP cc_start: 0.8411 (m-30) cc_final: 0.8208 (m-30)
REVERT: B  604 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.8127 (p90)
  outliers start: 18
  outliers final: 15
  residues processed: 131
  average time/residue: 0.0966
  time to fit residues: 17.5372
Evaluate side-chains
  133 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 116
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  196 ASP
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  480 ILE
Chi-restraints excluded: chain A residue  614 THR
Chi-restraints excluded: chain A residue  622 ASN
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  248 SER
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  337 ILE
Chi-restraints excluded: chain B residue  456 SER
Chi-restraints excluded: chain B residue  503 LYS
Chi-restraints excluded: chain B residue  604 PHE
Chi-restraints excluded: chain B residue  710 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 96 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 30 optimal weight:    0.8980
   chunk 0 optimal weight:    9.9990
   chunk 25 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 105 optimal weight:    2.9990
   chunk 106 optimal weight:    1.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
A 622 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.137842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.109296 restraints weight = 10129.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 1.73
r_work: 0.3024 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2891 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.1217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8792  Z= 0.149
  Angle     :  0.520   7.967  11852  Z= 0.260
  Chirality :  0.040   0.138   1414
  Planarity :  0.003   0.029   1454
  Dihedral  :  5.250  64.769   1178
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 11.03 %
    Favored  : 86.87 %
  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 aren not related in a simple way.
  whole:  2.24 (0.26), residues: 1090
  helix:  2.57 (0.19), residues: 734
  sheet:  1.27 (0.77), residues: 50
  loop : -1.32 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 472 
 TYR   0.011   0.001   TYR A 226 
 PHE   0.013   0.001   PHE A 604 
 TRP   0.003   0.001   TRP B 409 
 HIS   0.003   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 8792)
  covalent geometry    : angle       0.51986 (11852)
  hydrogen bonds       : bond        0.04902 (  577)
  hydrogen bonds       : angle       3.69461 ( 1695)

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 114
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A  248 SER cc_start: 0.8247 (m) cc_final: 0.7946 (m)
REVERT: A  457 ASN cc_start: 0.8555 (m-40) cc_final: 0.8253 (m110)
REVERT: A  584 ASN cc_start: 0.7057 (t0) cc_final: 0.6801 (t0)
REVERT: A  604 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.7961 (p90)
REVERT: B  166 LYS cc_start: 0.7171 (tttm) cc_final: 0.6709 (mtpp)
REVERT: B  208 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7420 (mt)
REVERT: B  244 MET cc_start: 0.8214 (mmm) cc_final: 0.7861 (mmm)
REVERT: B  603 ASP cc_start: 0.8418 (m-30) cc_final: 0.8215 (m-30)
  outliers start: 20
  outliers final: 16
  residues processed: 128
  average time/residue: 0.0966
  time to fit residues: 17.0565
Evaluate side-chains
  131 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  196 ASP
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  480 ILE
Chi-restraints excluded: chain A residue  604 PHE
Chi-restraints excluded: chain A residue  614 THR
Chi-restraints excluded: chain A residue  622 ASN
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  248 SER
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  337 ILE
Chi-restraints excluded: chain B residue  456 SER
Chi-restraints excluded: chain B residue  503 LYS
Chi-restraints excluded: chain B residue  566 SER
Chi-restraints excluded: chain B residue  710 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 102 optimal weight:    2.9990
   chunk 90 optimal weight:    6.9990
   chunk 54 optimal weight:   10.0000
   chunk 94 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 107 optimal weight:   20.0000
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 622 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.136324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.107561 restraints weight = 10307.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.3121 rms_B_bonded: 1.75
r_work: 0.3011 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2878 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.1244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8792  Z= 0.159
  Angle     :  0.527   6.254  11852  Z= 0.264
  Chirality :  0.040   0.138   1414
  Planarity :  0.003   0.029   1454
  Dihedral  :  5.288  66.505   1178
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 11.13 %
    Favored  : 86.76 %
  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:  2.20 (0.26), residues: 1090
  helix:  2.54 (0.19), residues: 734
  sheet:  1.26 (0.78), residues: 50
  loop : -1.36 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 494 
 TYR   0.011   0.001   TYR A 226 
 PHE   0.022   0.001   PHE B 604 
 TRP   0.003   0.001   TRP B 409 
 HIS   0.003   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 8792)
  covalent geometry    : angle       0.52693 (11852)
  hydrogen bonds       : bond        0.05025 (  577)
  hydrogen bonds       : angle       3.72220 ( 1695)

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 111
  time to evaluate  : 0.361 
Fit side-chains
REVERT: A  248 SER cc_start: 0.8267 (m) cc_final: 0.7979 (m)
REVERT: A  457 ASN cc_start: 0.8544 (m-40) cc_final: 0.8234 (m110)
REVERT: A  584 ASN cc_start: 0.7071 (t0) cc_final: 0.6092 (p0)
REVERT: A  604 PHE cc_start: 0.8512 (OUTLIER) cc_final: 0.7946 (p90)
REVERT: B  166 LYS cc_start: 0.7167 (tttm) cc_final: 0.6702 (mtpp)
REVERT: B  208 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7421 (mt)
REVERT: B  244 MET cc_start: 0.8238 (mmm) cc_final: 0.7850 (mmm)
REVERT: B  603 ASP cc_start: 0.8410 (m-30) cc_final: 0.8200 (m-30)
  outliers start: 20
  outliers final: 17
  residues processed: 125
  average time/residue: 0.0992
  time to fit residues: 17.1890
Evaluate side-chains
  129 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  196 ASP
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  480 ILE
Chi-restraints excluded: chain A residue  587 VAL
Chi-restraints excluded: chain A residue  604 PHE
Chi-restraints excluded: chain A residue  614 THR
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  248 SER
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  337 ILE
Chi-restraints excluded: chain B residue  420 MET
Chi-restraints excluded: chain B residue  456 SER
Chi-restraints excluded: chain B residue  503 LYS
Chi-restraints excluded: chain B residue  566 SER
Chi-restraints excluded: chain B residue  710 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 85 optimal weight:    0.0040
   chunk 8 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9980
   chunk 54 optimal weight:   10.0000
   chunk 52 optimal weight:    4.9990
   chunk 88 optimal weight:    0.5980
   chunk 104 optimal weight:    3.9990
   chunk 13 optimal weight:    0.0970
   chunk 96 optimal weight:    0.9990
   overall best weight:    0.5392

-------------------------------------------------------------------------------
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 = 0.3575 r_free = 0.3575 target = 0.143120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.115193 restraints weight = 10052.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3206 rms_B_bonded: 1.72
r_work: 0.3101 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2968 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.1282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8792  Z= 0.108
  Angle     :  0.487   7.239  11852  Z= 0.243
  Chirality :  0.039   0.160   1414
  Planarity :  0.002   0.028   1454
  Dihedral  :  5.163  58.362   1178
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 11.34 %
    Favored  : 86.76 %
  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:  2.34 (0.26), residues: 1090
  helix:  2.63 (0.19), residues: 744
  sheet:  1.24 (0.79), residues: 50
  loop : -1.35 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 472 
 TYR   0.010   0.001   TYR B 179 
 PHE   0.022   0.001   PHE B 604 
 TRP   0.004   0.001   TRP A 409 
 HIS   0.003   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 8792)
  covalent geometry    : angle       0.48655 (11852)
  hydrogen bonds       : bond        0.04299 (  577)
  hydrogen bonds       : angle       3.55437 ( 1695)

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

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

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2180 Ramachandran restraints generated.
    1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 0.393 
Fit side-chains
REVERT: A  155 MET cc_start: 0.6186 (tpt) cc_final: 0.5221 (mtm)
REVERT: A  190 ILE cc_start: 0.6439 (mt) cc_final: 0.6229 (mt)
REVERT: A  248 SER cc_start: 0.8141 (m) cc_final: 0.7868 (m)
REVERT: A  457 ASN cc_start: 0.8509 (m-40) cc_final: 0.8205 (m110)
REVERT: A  584 ASN cc_start: 0.7083 (t0) cc_final: 0.6171 (p0)
REVERT: A  604 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.7854 (p90)
REVERT: B  166 LYS cc_start: 0.7126 (tttm) cc_final: 0.6670 (mtpp)
REVERT: B  208 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7409 (mt)
REVERT: B  244 MET cc_start: 0.8098 (mmm) cc_final: 0.7804 (mmm)
REVERT: B  560 LYS cc_start: 0.8749 (mttt) cc_final: 0.7894 (mtpp)
REVERT: B  589 MET cc_start: 0.8690 (tpp) cc_final: 0.8430 (tpp)
REVERT: B  603 ASP cc_start: 0.8339 (m-30) cc_final: 0.8121 (m-30)
  outliers start: 18
  outliers final: 15
  residues processed: 130
  average time/residue: 0.1016
  time to fit residues: 18.0975
Evaluate side-chains
  131 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 114
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  196 ASP
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  587 VAL
Chi-restraints excluded: chain A residue  604 PHE
Chi-restraints excluded: chain A residue  614 THR
Chi-restraints excluded: chain A residue  699 VAL
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  248 SER
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  337 ILE
Chi-restraints excluded: chain B residue  420 MET
Chi-restraints excluded: chain B residue  456 SER
Chi-restraints excluded: chain B residue  485 ASP
Chi-restraints excluded: chain B residue  503 LYS
Chi-restraints excluded: chain B residue  710 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 79 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   chunk 82 optimal weight:    0.4980
   chunk 9 optimal weight:    2.9990
   chunk 105 optimal weight:    0.1980
   chunk 84 optimal weight:    3.9990
   chunk 63 optimal weight:    0.4980
   chunk 13 optimal weight:    0.8980
   chunk 96 optimal weight:    1.9990
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.3586 r_free = 0.3586 target = 0.143911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.115914 restraints weight = 9994.563|
|-----------------------------------------------------------------------------|
r_work (start): 0.3215 rms_B_bonded: 1.72
r_work: 0.3111 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.1361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8792  Z= 0.107
  Angle     :  0.475   5.822  11852  Z= 0.236
  Chirality :  0.039   0.150   1414
  Planarity :  0.002   0.028   1454
  Dihedral  :  5.111  55.403   1178
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 11.97 %
    Favored  : 86.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.45 (0.26), residues: 1090
  helix:  2.71 (0.19), residues: 744
  sheet:  1.34 (0.81), residues: 50
  loop : -1.33 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 494 
 TYR   0.010   0.001   TYR B 179 
 PHE   0.031   0.001   PHE B 604 
 TRP   0.003   0.000   TRP A 409 
 HIS   0.003   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 8792)
  covalent geometry    : angle       0.47532 (11852)
  hydrogen bonds       : bond        0.04206 (  577)
  hydrogen bonds       : angle       3.49491 ( 1695)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2289.17 seconds
wall clock time: 40 minutes 1.70 seconds (2401.70 seconds total)