Starting phenix.real_space_refine
on Mon Apr 28 06:03:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b4y_44191/04_2025/9b4y_44191.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b4y_44191/04_2025/9b4y_44191.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.74
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b4y_44191/04_2025/9b4y_44191.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b4y_44191/04_2025/9b4y_44191.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b4y_44191/04_2025/9b4y_44191.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b4y_44191/04_2025/9b4y_44191.cif"
  }
  resolution = 3.74
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.018
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      49      5.16       5
     C    4510      2.51       5
     N    1228      2.21       5
     O    1391      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 7178
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 876, 6810
          Classifications: {'peptide': 876}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 37, 'TRANS': 838}
    Chain: "B"
      Number of atoms: 368
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 368
          Classifications: {'peptide': 43}
          Link IDs: {'TRANS': 42}
  Time building chain proxies: 4.78, per 1000 atoms: 0.67
  Number of scatterers: 7178
  At special positions: 0
  Unit cell: (100.28, 109, 84.584, 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      49     16.00
     O    1391      8.00
     N    1228      7.00
     C    4510      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: 1.82
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1760

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 0 sheets defined
      84.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.76
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 10
      removed outlier: 3.551A  pdb=" N   ILE A   6 " --> pdb=" O   GLU A   2 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 14 through 32
    Processing helix  chain 'A' and resid 32 through 46
      removed outlier: 3.607A  pdb=" N   ASN A  46 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 66
    Processing helix  chain 'A' and resid 69 through 82
    Processing helix  chain 'A' and resid 84 through 99
      removed outlier: 3.877A  pdb=" N   LEU A  99 " --> pdb=" O   VAL A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 124
      removed outlier: 4.168A  pdb=" N   GLN A 111 " --> pdb=" O   SER A 107 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   CYS A 112 " --> pdb=" O   SER A 108 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   ALA A 119 " --> pdb=" O   GLY A 115 " (cutoff:3.500A)
      Proline residue:  A 122  - end of helix
    Processing helix  chain 'A' and resid 128 through 139
    Processing helix  chain 'A' and resid 143 through 161
    Processing helix  chain 'A' and resid 162 through 168
      removed outlier: 5.216A  pdb=" N   ASP A 168 " --> pdb=" O   GLN A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 180
      removed outlier: 3.641A  pdb=" N   ILE A 173 " --> pdb=" O   LYS A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 201
      removed outlier: 3.868A  pdb=" N   LYS A 191 " --> pdb=" O   SER A 187 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   SER A 201 " --> pdb=" O   ALA A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 210
    Processing helix  chain 'A' and resid 211 through 226
      removed outlier: 3.519A  pdb=" N   VAL A 221 " --> pdb=" O   PHE A 217 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   VAL A 222 " --> pdb=" O   ILE A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 248
    Processing helix  chain 'A' and resid 249 through 256
      removed outlier: 3.659A  pdb=" N   MET A 252 " --> pdb=" O   TYR A 249 " (cutoff:3.500A)
      removed outlier: 5.446A  pdb=" N   GLU A 253 " --> pdb=" O   GLN A 250 " (cutoff:3.500A)
      removed outlier: 4.534A  pdb=" N   THR A 254 " --> pdb=" O   TYR A 251 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   TYR A 255 " --> pdb=" O   MET A 252 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   MET A 256 " --> pdb=" O   GLU A 253 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 249 through 256'
    Processing helix  chain 'A' and resid 259 through 269
      removed outlier: 4.266A  pdb=" N   ILE A 263 " --> pdb=" O   ALA A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 304
      removed outlier: 3.639A  pdb=" N   ALA A 276 " --> pdb=" O   ILE A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 330
      Proline residue:  A 324  - end of helix
    Processing helix  chain 'A' and resid 343 through 360
      removed outlier: 3.610A  pdb=" N   GLY A 349 " --> pdb=" O   CYS A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 375
      Proline residue:  A 369  - end of helix
    Processing helix  chain 'A' and resid 379 through 393
      removed outlier: 3.697A  pdb=" N   ARG A 383 " --> pdb=" O   ASP A 379 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ALA A 385 " --> pdb=" O   ARG A 381 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   PHE A 390 " --> pdb=" O   ALA A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 417
      removed outlier: 3.563A  pdb=" N   LEU A 402 " --> pdb=" O   GLU A 398 " (cutoff:3.500A)
      Proline residue:  A 404  - end of helix
      removed outlier: 3.666A  pdb=" N   GLN A 408 " --> pdb=" O   PRO A 404 " (cutoff:3.500A)
      Proline residue:  A 411  - end of helix
      removed outlier: 3.603A  pdb=" N   GLU A 415 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 439
      removed outlier: 3.538A  pdb=" N   TRP A 430 " --> pdb=" O   ASP A 426 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 444
      removed outlier: 3.544A  pdb=" N   ILE A 444 " --> pdb=" O   PRO A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 460
      removed outlier: 4.259A  pdb=" N   ALA A 450 " --> pdb=" O   ASP A 446 " (cutoff:3.500A)
      Proline residue:  A 451  - end of helix
    Processing helix  chain 'A' and resid 463 through 489
      removed outlier: 4.030A  pdb=" N   ASN A 469 " --> pdb=" O   ARG A 465 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   TRP A 472 " --> pdb=" O   SER A 468 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   ALA A 473 " --> pdb=" O   ASN A 469 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   VAL A 487 " --> pdb=" O   GLU A 483 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ALA A 488 " --> pdb=" O   ALA A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 514
      removed outlier: 4.467A  pdb=" N   GLU A 504 " --> pdb=" O   SER A 500 " (cutoff:3.500A)
      removed outlier: 5.457A  pdb=" N   LEU A 505 " --> pdb=" O   SER A 501 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   GLN A 508 " --> pdb=" O   GLU A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 522
      No H-bonds generated for 'chain 'A' and resid 520 through 522'
    Processing helix  chain 'A' and resid 523 through 538
    Processing helix  chain 'A' and resid 540 through 542
      No H-bonds generated for 'chain 'A' and resid 540 through 542'
    Processing helix  chain 'A' and resid 543 through 563
      removed outlier: 3.704A  pdb=" N   GLN A 563 " --> pdb=" O   GLN A 559 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 570 through 593
    Processing helix  chain 'A' and resid 596 through 618
      removed outlier: 3.652A  pdb=" N   LEU A 601 " --> pdb=" O   HIS A 597 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   GLN A 602 " --> pdb=" O   GLN A 598 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   ILE A 603 " --> pdb=" O   ASP A 599 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   ASP A 605 " --> pdb=" O   LEU A 601 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   VAL A 606 " --> pdb=" O   GLN A 602 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   THR A 618 " --> pdb=" O   MET A 614 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 640
      removed outlier: 4.298A  pdb=" N   GLN A 625 " --> pdb=" O   SER A 621 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLU A 626 " --> pdb=" O   GLY A 622 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   ASP A 627 " --> pdb=" O   GLY A 623 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   MET A 630 " --> pdb=" O   GLU A 626 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 642 through 646
      removed outlier: 3.933A  pdb=" N   LYS A 645 " --> pdb=" O   GLU A 642 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 650 through 659
      removed outlier: 3.510A  pdb=" N   LEU A 658 " --> pdb=" O   LEU A 654 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 663 through 682
      removed outlier: 4.047A  pdb=" N   CYS A 667 " --> pdb=" O   GLU A 663 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   GLY A 672 " --> pdb=" O   LEU A 668 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 685 through 702
      removed outlier: 4.193A  pdb=" N   ASP A 690 " --> pdb=" O   ILE A 686 " (cutoff:3.500A)
      removed outlier: 5.065A  pdb=" N   GLU A 691 " --> pdb=" O   PRO A 687 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   VAL A 692 " --> pdb=" O   PHE A 688 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LEU A 695 " --> pdb=" O   GLU A 691 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LEU A 700 " --> pdb=" O   LEU A 696 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 708 through 725
      removed outlier: 4.307A  pdb=" N   GLN A 712 " --> pdb=" O   SER A 708 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   PHE A 717 " --> pdb=" O   ILE A 713 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   GLY A 718 " --> pdb=" O   LEU A 714 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   ASP A 719 " --> pdb=" O   SER A 715 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ILE A 720 " --> pdb=" O   VAL A 716 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   ALA A 721 " --> pdb=" O   PHE A 717 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LEU A 722 " --> pdb=" O   GLY A 718 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ALA A 723 " --> pdb=" O   ASP A 719 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 728 through 745
      removed outlier: 4.506A  pdb=" N   GLU A 733 " --> pdb=" O   LYS A 729 " (cutoff:3.500A)
      removed outlier: 5.917A  pdb=" N   VAL A 734 " --> pdb=" O   LYS A 730 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ASN A 737 " --> pdb=" O   GLU A 733 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ALA A 745 " --> pdb=" O   GLN A 741 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 751 through 778
      removed outlier: 3.756A  pdb=" N   ASN A 759 " --> pdb=" O   VAL A 755 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 784 through 789
    Processing helix  chain 'A' and resid 793 through 807
    Processing helix  chain 'A' and resid 811 through 829
      removed outlier: 3.542A  pdb=" N   CYS A 817 " --> pdb=" O   GLY A 813 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ALA A 819 " --> pdb=" O   VAL A 815 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 830 through 839
      removed outlier: 4.007A  pdb=" N   LYS A 835 " --> pdb=" O   LYS A 831 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   LEU A 836 " --> pdb=" O   ASP A 832 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ALA A 839 " --> pdb=" O   LYS A 835 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 841 through 853
      removed outlier: 3.679A  pdb=" N   GLY A 850 " --> pdb=" O   LEU A 846 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ARG A 851 " --> pdb=" O   LEU A 847 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ARG A 852 " --> pdb=" O   THR A 848 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 855 through 874
      removed outlier: 3.530A  pdb=" N   GLU A 868 " --> pdb=" O   TRP A 864 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 13 through 17
      removed outlier: 3.593A  pdb=" N   PHE B  17 " --> pdb=" O   LEU B  14 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 23 through 52
      removed outlier: 3.553A  pdb=" N   ARG B  29 " --> pdb=" O   THR B  25 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ARG B  30 " --> pdb=" O   GLU B  26 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   VAL B  34 " --> pdb=" O   ARG B  30 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ARG B  50 " --> pdb=" O   GLN B  46 " (cutoff:3.500A)

    479 hydrogen bonds defined for protein.
    1413 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.28

  Time building geometry restraints manager: 2.20 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2443
        1.35 -     1.46: 1392
        1.46 -     1.58: 3381
        1.58 -     1.69: 0
        1.69 -     1.81: 75
  Bond restraints: 7291
  Sorted by residual:
  bond pdb=" N   LYS B  18 "
       pdb=" CA  LYS B  18 "
    ideal  model  delta    sigma   weight residual
    1.457  1.468 -0.011 1.29e-02 6.01e+03 6.80e-01
  bond pdb=" C   LEU A 368 "
       pdb=" N   PRO A 369 "
    ideal  model  delta    sigma   weight residual
    1.335  1.343 -0.008 1.28e-02 6.10e+03 4.25e-01
  bond pdb=" C   LYS B  18 "
       pdb=" O   LYS B  18 "
    ideal  model  delta    sigma   weight residual
    1.235  1.243 -0.008 1.26e-02 6.30e+03 3.87e-01
  bond pdb=" C   ILE A 121 "
       pdb=" N   PRO A 122 "
    ideal  model  delta    sigma   weight residual
    1.335  1.342 -0.008 1.28e-02 6.10e+03 3.63e-01
  bond pdb=" CA  VAL A 323 "
       pdb=" C   VAL A 323 "
    ideal  model  delta    sigma   weight residual
    1.523  1.529 -0.006 9.20e-03 1.18e+04 3.59e-01
  ... (remaining 7286 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.78: 9760
        1.78 -     3.55: 96
        3.55 -     5.33: 24
        5.33 -     7.11: 1
        7.11 -     8.88: 1
  Bond angle restraints: 9882
  Sorted by residual:
  angle pdb=" N   GLN A 569 "
        pdb=" CA  GLN A 569 "
        pdb=" C   GLN A 569 "
      ideal   model   delta    sigma   weight residual
     114.56  109.85    4.71 1.27e+00 6.20e-01 1.38e+01
  angle pdb=" C   LEU A 129 "
        pdb=" N   ILE A 130 "
        pdb=" CA  ILE A 130 "
      ideal   model   delta    sigma   weight residual
     120.33  123.19   -2.86 8.00e-01 1.56e+00 1.27e+01
  angle pdb=" C   LYS B  18 "
        pdb=" CA  LYS B  18 "
        pdb=" CB  LYS B  18 "
      ideal   model   delta    sigma   weight residual
     110.42  115.69   -5.27 1.99e+00 2.53e-01 7.00e+00
  angle pdb=" C   LEU A 322 "
        pdb=" N   VAL A 323 "
        pdb=" CA  VAL A 323 "
      ideal   model   delta    sigma   weight residual
     120.33  122.43   -2.10 8.00e-01 1.56e+00 6.86e+00
  angle pdb=" CA  LEU A 368 "
        pdb=" CB  LEU A 368 "
        pdb=" CG  LEU A 368 "
      ideal   model   delta    sigma   weight residual
     116.30  125.18   -8.88 3.50e+00 8.16e-02 6.44e+00
  ... (remaining 9877 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.46: 4180
       16.46 -    32.92: 247
       32.92 -    49.39: 63
       49.39 -    65.85: 17
       65.85 -    82.31: 6
  Dihedral angle restraints: 4513
    sinusoidal: 1813
      harmonic: 2700
  Sorted by residual:
  dihedral pdb=" N   CYS A 287 "
           pdb=" CA  CYS A 287 "
           pdb=" CB  CYS A 287 "
           pdb=" SG  CYS A 287 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  120.07   59.93     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" N   GLU A 398 "
           pdb=" CA  GLU A 398 "
           pdb=" CB  GLU A 398 "
           pdb=" CG  GLU A 398 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  120.48   59.52     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" N   MET A 181 "
           pdb=" CA  MET A 181 "
           pdb=" CB  MET A 181 "
           pdb=" CG  MET A 181 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -121.51  -58.49     3      1.50e+01 4.44e-03 9.47e+00
  ... (remaining 4510 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 691
       0.027 -    0.054: 315
       0.054 -    0.080: 93
       0.080 -    0.107: 47
       0.107 -    0.134: 1
  Chirality restraints: 1147
  Sorted by residual:
  chirality pdb=" CA  LEU A 368 "
            pdb=" N   LEU A 368 "
            pdb=" C   LEU A 368 "
            pdb=" CB  LEU A 368 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.50e-01
  chirality pdb=" CA  PRO A 258 "
            pdb=" N   PRO A 258 "
            pdb=" C   PRO A 258 "
            pdb=" CB  PRO A 258 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.61    0.11 2.00e-01 2.50e+01 2.87e-01
  chirality pdb=" CA  PRO A 399 "
            pdb=" N   PRO A 399 "
            pdb=" C   PRO A 399 "
            pdb=" CB  PRO A 399 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.61    0.11 2.00e-01 2.50e+01 2.82e-01
  ... (remaining 1144 not shown)

  Planarity restraints: 1292
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 396 "   -0.035 5.00e-02 4.00e+02   5.28e-02 4.46e+00
        pdb=" N   PRO A 397 "    0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO A 397 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 397 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 410 "    0.016 5.00e-02 4.00e+02   2.37e-02 9.02e-01
        pdb=" N   PRO A 411 "   -0.041 5.00e-02 4.00e+02
        pdb=" CA  PRO A 411 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A 411 "    0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 185 "   -0.013 5.00e-02 4.00e+02   2.02e-02 6.51e-01
        pdb=" N   PRO A 186 "    0.035 5.00e-02 4.00e+02
        pdb=" CA  PRO A 186 "   -0.010 5.00e-02 4.00e+02
        pdb=" CD  PRO A 186 "   -0.011 5.00e-02 4.00e+02
  ... (remaining 1289 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 543
        2.74 -     3.28: 8181
        3.28 -     3.82: 12139
        3.82 -     4.36: 14476
        4.36 -     4.90: 22803
  Nonbonded interactions: 58142
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 618 "
            pdb=" O   GLY A 620 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" OE2 GLU A 398 "
            pdb=" OG  SER A 400 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" O   ALA A 600 "
            pdb=" OG  SER A 604 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   ALA A 631 "
            pdb=" OG1 THR A 634 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" OG1 THR A 827 "
            pdb=" OE2 GLU A 868 "
     model   vdw
     2.300 3.040
  ... (remaining 58137 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: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.350
  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:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.260
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   7291  Z= 0.094
  Angle     :  0.523   8.884   9882  Z= 0.302
  Chirality :  0.035   0.134   1147
  Planarity :  0.003   0.053   1292
  Dihedral  : 12.309  82.309   2753
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  :  7.72 %
    Favored  : 87.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.29), residues: 915
  helix:  0.70 (0.21), residues: 683
  sheet:  None (None), residues: 0
  loop : -0.27 (0.45), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 342 
 HIS   0.002   0.000   HIS A 374 
 PHE   0.008   0.001   PHE A 204 
 TYR   0.005   0.001   TYR A 661 
 ARG   0.002   0.000   ARG A 593 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.26626 (  479)
  hydrogen bonds       : angle       6.71487 ( 1413)
  covalent geometry    : bond        0.00168 ( 7291)
  covalent geometry    : angle       0.52340 ( 9882)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 191
  time to evaluate  : 0.844 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.9391 (tmm) cc_final: 0.9120 (tmm)
REVERT: A   80 TRP cc_start: 0.8024 (t-100) cc_final: 0.7613 (t-100)
REVERT: A  146 MET cc_start: 0.9193 (tmm) cc_final: 0.8857 (tmm)
REVERT: A  162 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.7351 (p0)
REVERT: A  206 LYS cc_start: 0.9416 (ptpp) cc_final: 0.9055 (tptp)
REVERT: A  240 ASN cc_start: 0.8991 (t0) cc_final: 0.8568 (t0)
REVERT: A  281 GLU cc_start: 0.8872 (tp30) cc_final: 0.8088 (tp30)
REVERT: A  282 PHE cc_start: 0.8643 (t80) cc_final: 0.8381 (t80)
REVERT: A  285 ASN cc_start: 0.9013 (m-40) cc_final: 0.8451 (m-40)
REVERT: A  290 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8403 (tp30)
REVERT: A  416 LEU cc_start: 0.9299 (mt) cc_final: 0.8812 (mt)
REVERT: A  472 TRP cc_start: 0.7782 (m-90) cc_final: 0.7339 (m-90)
REVERT: A  634 THR cc_start: 0.9459 (p) cc_final: 0.8723 (p)
REVERT: A  643 PHE cc_start: 0.8499 (t80) cc_final: 0.8263 (t80)
REVERT: A  714 LEU cc_start: 0.9588 (mt) cc_final: 0.9326 (mt)
REVERT: A  717 PHE cc_start: 0.8450 (m-10) cc_final: 0.7392 (m-80)
REVERT: A  728 PHE cc_start: 0.7831 (t80) cc_final: 0.7219 (t80)
REVERT: B   24 SER cc_start: 0.9236 (m) cc_final: 0.8938 (p)
REVERT: B   25 THR cc_start: 0.9156 (p) cc_final: 0.8627 (p)
REVERT: B   27 MET cc_start: 0.8950 (mmm) cc_final: 0.8042 (mmm)
REVERT: B   28 ARG cc_start: 0.8702 (mmm-85) cc_final: 0.8497 (ttt180)
REVERT: B   30 ARG cc_start: 0.9072 (mtp85) cc_final: 0.8357 (mtp85)
  outliers start: 38
  outliers final: 11
  residues processed: 219
  average time/residue: 0.2207
  time to fit residues: 62.3990
Evaluate side-chains
  149 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 136
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 ASP
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  255 TYR
Chi-restraints excluded: chain A residue  261 PHE
Chi-restraints excluded: chain A residue  273 ASP
Chi-restraints excluded: chain A residue  287 CYS
Chi-restraints excluded: chain A residue  290 GLU
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  414 ILE
Chi-restraints excluded: chain A residue  614 MET
Chi-restraints excluded: chain A residue  618 THR
Chi-restraints excluded: chain A residue  863 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    6.9990
   chunk 68 optimal weight:    0.4980
   chunk 38 optimal weight:    1.9990
   chunk 23 optimal weight:    7.9990
   chunk 46 optimal weight:   10.0000
   chunk 36 optimal weight:    4.9990
   chunk 71 optimal weight:    6.9990
   chunk 27 optimal weight:    9.9990
   chunk 43 optimal weight:    0.9980
   chunk 53 optimal weight:    5.9990
   chunk 82 optimal weight:    0.6980
   overall best weight:    1.8384

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

Flipped N/Q/H residues before XYZ refinement:
A  22 GLN
A  77 GLN
** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 GLN
A 454 GLN
** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 521 GLN
A 522 ASN
A 548 GLN
A 576 GLN
A 590 ASN
A 660 ASN
A 682 GLN
A 740 GLN
A 744 GLN
A 774 GLN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.055032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.041236 restraints weight = 55572.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.042191 restraints weight = 39475.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.042881 restraints weight = 30708.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.2849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7291  Z= 0.175
  Angle     :  0.826  13.502   9882  Z= 0.396
  Chirality :  0.044   0.176   1147
  Planarity :  0.005   0.059   1292
  Dihedral  :  6.154  55.090   1011
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 15.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 15.70 %
    Favored  : 81.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.28), residues: 915
  helix:  0.54 (0.19), residues: 703
  sheet:  None (None), residues: 0
  loop : -0.30 (0.47), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  80 
 HIS   0.003   0.001   HIS A  97 
 PHE   0.021   0.001   PHE A 503 
 TYR   0.016   0.001   TYR A 248 
 ARG   0.005   0.001   ARG A 525 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05926 (  479)
  hydrogen bonds       : angle       5.01055 ( 1413)
  covalent geometry    : bond        0.00348 ( 7291)
  covalent geometry    : angle       0.82614 ( 9882)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 155
  time to evaluate  : 0.793 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 TRP cc_start: 0.8473 (t-100) cc_final: 0.7932 (t-100)
REVERT: A   99 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7159 (pt)
REVERT: A  146 MET cc_start: 0.9514 (tmm) cc_final: 0.9184 (tmm)
REVERT: A  239 GLN cc_start: 0.9718 (tt0) cc_final: 0.9313 (tm-30)
REVERT: A  240 ASN cc_start: 0.9691 (t0) cc_final: 0.9242 (m-40)
REVERT: A  252 MET cc_start: 0.9512 (mmm) cc_final: 0.9306 (mmm)
REVERT: A  281 GLU cc_start: 0.9289 (tp30) cc_final: 0.8672 (tp30)
REVERT: A  282 PHE cc_start: 0.9568 (t80) cc_final: 0.9260 (t80)
REVERT: A  287 CYS cc_start: 0.9354 (OUTLIER) cc_final: 0.9138 (t)
REVERT: A  353 MET cc_start: 0.9299 (tpp) cc_final: 0.8680 (tpt)
REVERT: A  438 LEU cc_start: 0.9503 (mp) cc_final: 0.9248 (mp)
REVERT: A  589 GLN cc_start: 0.9729 (mt0) cc_final: 0.9318 (mp10)
REVERT: A  643 PHE cc_start: 0.9585 (t80) cc_final: 0.9064 (t80)
REVERT: A  650 PHE cc_start: 0.9654 (t80) cc_final: 0.9314 (t80)
REVERT: A  728 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.8266 (t80)
REVERT: B   22 LYS cc_start: 0.6775 (mmmm) cc_final: 0.6275 (mppt)
REVERT: B   45 ASP cc_start: 0.9443 (t0) cc_final: 0.9187 (t0)
REVERT: B   49 LYS cc_start: 0.9108 (pttp) cc_final: 0.8697 (pttp)
  outliers start: 23
  outliers final: 9
  residues processed: 169
  average time/residue: 0.2242
  time to fit residues: 48.9810
Evaluate side-chains
  139 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 127
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  255 TYR
Chi-restraints excluded: chain A residue  287 CYS
Chi-restraints excluded: chain A residue  288 ASP
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  414 ILE
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  728 PHE
Chi-restraints excluded: chain A residue  863 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 5 optimal weight:   30.0000
   chunk 78 optimal weight:    5.9990
   chunk 41 optimal weight:    0.0670
   chunk 83 optimal weight:    0.9980
   chunk 34 optimal weight:   20.0000
   chunk 3 optimal weight:    8.9990
   chunk 46 optimal weight:    9.9990
   chunk 84 optimal weight:    0.9990
   chunk 50 optimal weight:    7.9990
   chunk 21 optimal weight:    9.9990
   chunk 61 optimal weight:    7.9990
   overall best weight:    3.2124

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

Flipped N/Q/H residues before XYZ refinement:
A 189 ASN
A 196 ASN
A 208 ASN
** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 520 HIS
A 596 GLN
A 740 GLN
A 744 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.053928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.039854 restraints weight = 56540.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.040767 restraints weight = 41412.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.041444 restraints weight = 32867.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.3459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   7291  Z= 0.164
  Angle     :  0.820  15.703   9882  Z= 0.382
  Chirality :  0.043   0.182   1147
  Planarity :  0.005   0.067   1292
  Dihedral  :  5.498  53.641    997
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 16.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 17.22 %
    Favored  : 79.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.28), residues: 915
  helix:  0.64 (0.20), residues: 693
  sheet:  None (None), residues: 0
  loop :  0.04 (0.48), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  80 
 HIS   0.003   0.001   HIS A  97 
 PHE   0.020   0.002   PHE A 503 
 TYR   0.017   0.001   TYR A 248 
 ARG   0.008   0.001   ARG B  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04765 (  479)
  hydrogen bonds       : angle       4.85381 ( 1413)
  covalent geometry    : bond        0.00352 ( 7291)
  covalent geometry    : angle       0.82025 ( 9882)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 144
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 TRP cc_start: 0.8609 (t-100) cc_final: 0.8036 (t-100)
REVERT: A  146 MET cc_start: 0.9535 (tmm) cc_final: 0.9220 (tmm)
REVERT: A  239 GLN cc_start: 0.9698 (tt0) cc_final: 0.9474 (pt0)
REVERT: A  241 LEU cc_start: 0.9791 (tp) cc_final: 0.9575 (tp)
REVERT: A  281 GLU cc_start: 0.9279 (tp30) cc_final: 0.8648 (tp30)
REVERT: A  282 PHE cc_start: 0.9528 (t80) cc_final: 0.9059 (t80)
REVERT: A  287 CYS cc_start: 0.9417 (OUTLIER) cc_final: 0.8984 (t)
REVERT: A  291 MET cc_start: 0.9003 (mmm) cc_final: 0.8773 (mmm)
REVERT: A  353 MET cc_start: 0.9268 (tpp) cc_final: 0.9060 (tpp)
REVERT: A  388 MET cc_start: 0.9439 (tpp) cc_final: 0.9109 (tpp)
REVERT: A  436 CYS cc_start: 0.9676 (m) cc_final: 0.9153 (t)
REVERT: A  589 GLN cc_start: 0.9700 (mt0) cc_final: 0.9278 (mp10)
REVERT: A  614 MET cc_start: 0.9228 (tpp) cc_final: 0.8780 (mmt)
REVERT: A  634 THR cc_start: 0.9736 (p) cc_final: 0.9487 (p)
REVERT: A  643 PHE cc_start: 0.9576 (t80) cc_final: 0.9057 (t80)
REVERT: A  650 PHE cc_start: 0.9626 (t80) cc_final: 0.9192 (t80)
REVERT: A  717 PHE cc_start: 0.8939 (m-10) cc_final: 0.7771 (m-80)
REVERT: A  728 PHE cc_start: 0.8639 (OUTLIER) cc_final: 0.8337 (t80)
REVERT: B   18 LYS cc_start: 0.9163 (ttmm) cc_final: 0.8835 (ttmm)
REVERT: B   22 LYS cc_start: 0.6755 (mmmm) cc_final: 0.6271 (mppt)
REVERT: B   28 ARG cc_start: 0.9390 (ttt-90) cc_final: 0.9177 (ttt180)
  outliers start: 23
  outliers final: 14
  residues processed: 161
  average time/residue: 0.2141
  time to fit residues: 45.1092
Evaluate side-chains
  146 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 130
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  208 ASN
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  255 TYR
Chi-restraints excluded: chain A residue  273 ASP
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  287 CYS
Chi-restraints excluded: chain A residue  288 ASP
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  414 ILE
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  692 VAL
Chi-restraints excluded: chain A residue  728 PHE
Chi-restraints excluded: chain A residue  863 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 81 optimal weight:   30.0000
   chunk 72 optimal weight:    8.9990
   chunk 35 optimal weight:    4.9990
   chunk 64 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 20 optimal weight:    7.9990
   chunk 54 optimal weight:    6.9990
   chunk 36 optimal weight:    0.0470
   chunk 61 optimal weight:    1.9990
   chunk 11 optimal weight:    7.9990
   chunk 55 optimal weight:    6.9990
   overall best weight:    2.8086

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

Flipped N/Q/H residues before XYZ refinement:
A 208 ASN
** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 523 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.093501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.079268 restraints weight = 57339.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.080796 restraints weight = 26269.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.081713 restraints weight = 15241.719|
|-----------------------------------------------------------------------------|
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.3823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   7291  Z= 0.154
  Angle     :  0.792  16.631   9882  Z= 0.375
  Chirality :  0.044   0.226   1147
  Planarity :  0.004   0.060   1292
  Dihedral  :  5.461  52.741    997
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 17.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 18.99 %
    Favored  : 78.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.29), residues: 915
  helix:  0.60 (0.20), residues: 698
  sheet:  None (None), residues: 0
  loop : -0.08 (0.48), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 430 
 HIS   0.003   0.001   HIS A  97 
 PHE   0.025   0.002   PHE A 503 
 TYR   0.011   0.001   TYR A 248 
 ARG   0.016   0.001   ARG A 593 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04323 (  479)
  hydrogen bonds       : angle       4.79480 ( 1413)
  covalent geometry    : bond        0.00341 ( 7291)
  covalent geometry    : angle       0.79230 ( 9882)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 140
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 TRP cc_start: 0.8495 (t-100) cc_final: 0.7926 (t-100)
REVERT: A  146 MET cc_start: 0.9560 (tmm) cc_final: 0.9260 (tmm)
REVERT: A  252 MET cc_start: 0.9430 (mmm) cc_final: 0.9216 (mmm)
REVERT: A  281 GLU cc_start: 0.9173 (tp30) cc_final: 0.8565 (tp30)
REVERT: A  287 CYS cc_start: 0.9424 (OUTLIER) cc_final: 0.8933 (t)
REVERT: A  353 MET cc_start: 0.9457 (tpp) cc_final: 0.8859 (tpp)
REVERT: A  388 MET cc_start: 0.9410 (tpp) cc_final: 0.9041 (tpp)
REVERT: A  436 CYS cc_start: 0.9661 (m) cc_final: 0.9214 (t)
REVERT: A  503 PHE cc_start: 0.9495 (t80) cc_final: 0.8897 (t80)
REVERT: A  509 LYS cc_start: 0.9800 (mmmt) cc_final: 0.9590 (mmmt)
REVERT: A  533 MET cc_start: 0.9596 (mtt) cc_final: 0.9313 (mmt)
REVERT: A  568 ILE cc_start: 0.7079 (OUTLIER) cc_final: 0.6678 (mm)
REVERT: A  589 GLN cc_start: 0.9624 (mt0) cc_final: 0.9409 (mp10)
REVERT: A  614 MET cc_start: 0.9103 (tpp) cc_final: 0.8689 (mmt)
REVERT: A  643 PHE cc_start: 0.9555 (t80) cc_final: 0.9020 (t80)
REVERT: A  650 PHE cc_start: 0.9604 (t80) cc_final: 0.9166 (t80)
REVERT: A  728 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8487 (t80)
REVERT: B   18 LYS cc_start: 0.9040 (ttmm) cc_final: 0.8681 (ttmm)
REVERT: B   22 LYS cc_start: 0.7160 (mmmm) cc_final: 0.6641 (mppt)
REVERT: B   26 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8167 (pp20)
REVERT: B   27 MET cc_start: 0.9504 (mmm) cc_final: 0.8990 (mmm)
REVERT: B   28 ARG cc_start: 0.9330 (ttt-90) cc_final: 0.9067 (ttt180)
REVERT: B   30 ARG cc_start: 0.9610 (mtp85) cc_final: 0.9276 (ttm110)
  outliers start: 22
  outliers final: 13
  residues processed: 156
  average time/residue: 0.2143
  time to fit residues: 43.9982
Evaluate side-chains
  148 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 132
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  208 ASN
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  255 TYR
Chi-restraints excluded: chain A residue  273 ASP
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  287 CYS
Chi-restraints excluded: chain A residue  288 ASP
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  448 TYR
Chi-restraints excluded: chain A residue  568 ILE
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  728 PHE
Chi-restraints excluded: chain A residue  863 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 43 optimal weight:    0.7980
   chunk 14 optimal weight:    0.0570
   chunk 33 optimal weight:   20.0000
   chunk 28 optimal weight:    5.9990
   chunk 70 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 17 optimal weight:    4.9990
   chunk 21 optimal weight:    8.9990
   chunk 54 optimal weight:    2.9990
   chunk 79 optimal weight:    6.9990
   overall best weight:    2.3704

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

Flipped N/Q/H residues before XYZ refinement:
** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.081572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.074431 restraints weight = 54003.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.075807 restraints weight = 24233.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.076614 restraints weight = 13565.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.4034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7291  Z= 0.141
  Angle     :  0.796  18.378   9882  Z= 0.374
  Chirality :  0.044   0.246   1147
  Planarity :  0.004   0.059   1292
  Dihedral  :  5.405  52.383    995
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 18.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 20.89 %
    Favored  : 76.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.29), residues: 915
  helix:  0.58 (0.20), residues: 696
  sheet:  None (None), residues: 0
  loop : -0.05 (0.48), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 430 
 HIS   0.003   0.001   HIS B  15 
 PHE   0.022   0.002   PHE A 503 
 TYR   0.013   0.001   TYR A 248 
 ARG   0.009   0.001   ARG A 593 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04136 (  479)
  hydrogen bonds       : angle       4.70514 ( 1413)
  covalent geometry    : bond        0.00306 ( 7291)
  covalent geometry    : angle       0.79596 ( 9882)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 137
  time to evaluate  : 0.801 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 TRP cc_start: 0.8469 (t-100) cc_final: 0.7894 (t-100)
REVERT: A  146 MET cc_start: 0.9570 (tmm) cc_final: 0.9253 (tmm)
REVERT: A  239 GLN cc_start: 0.9680 (tt0) cc_final: 0.9354 (tm-30)
REVERT: A  252 MET cc_start: 0.9445 (mmm) cc_final: 0.9177 (mmm)
REVERT: A  281 GLU cc_start: 0.9162 (tp30) cc_final: 0.8630 (tp30)
REVERT: A  282 PHE cc_start: 0.9511 (t80) cc_final: 0.9140 (t80)
REVERT: A  287 CYS cc_start: 0.9374 (OUTLIER) cc_final: 0.8924 (t)
REVERT: A  353 MET cc_start: 0.9534 (tpp) cc_final: 0.8901 (tpp)
REVERT: A  388 MET cc_start: 0.9416 (tpp) cc_final: 0.9047 (tpp)
REVERT: A  436 CYS cc_start: 0.9701 (m) cc_final: 0.9320 (t)
REVERT: A  503 PHE cc_start: 0.9571 (t80) cc_final: 0.9049 (t80)
REVERT: A  529 TYR cc_start: 0.8471 (m-80) cc_final: 0.7877 (m-80)
REVERT: A  533 MET cc_start: 0.9600 (mtt) cc_final: 0.9285 (mmm)
REVERT: A  568 ILE cc_start: 0.7066 (OUTLIER) cc_final: 0.6728 (mm)
REVERT: A  589 GLN cc_start: 0.9643 (mt0) cc_final: 0.9397 (mp10)
REVERT: A  614 MET cc_start: 0.9184 (tpp) cc_final: 0.8813 (mmt)
REVERT: A  643 PHE cc_start: 0.9510 (t80) cc_final: 0.9003 (t80)
REVERT: A  650 PHE cc_start: 0.9660 (t80) cc_final: 0.9220 (t80)
REVERT: A  728 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8572 (t80)
REVERT: B   18 LYS cc_start: 0.8933 (ttmm) cc_final: 0.8527 (ttmm)
REVERT: B   22 LYS cc_start: 0.6975 (mmmm) cc_final: 0.6366 (mppt)
REVERT: B   26 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8238 (tm-30)
REVERT: B   27 MET cc_start: 0.9517 (mmm) cc_final: 0.9212 (mmm)
  outliers start: 21
  outliers final: 14
  residues processed: 150
  average time/residue: 0.2102
  time to fit residues: 41.1151
Evaluate side-chains
  146 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 129
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  255 TYR
Chi-restraints excluded: chain A residue  273 ASP
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  287 CYS
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  410 MET
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  448 TYR
Chi-restraints excluded: chain A residue  568 ILE
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  728 PHE
Chi-restraints excluded: chain A residue  863 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 66 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 13 optimal weight:    6.9990
   chunk 24 optimal weight:    4.9990
   chunk 7 optimal weight:    5.9990
   chunk 17 optimal weight:    8.9990
   chunk 32 optimal weight:    6.9990
   chunk 57 optimal weight:    3.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 208 ASN
** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.080436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.073175 restraints weight = 55173.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.074576 restraints weight = 24642.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.075362 restraints weight = 13736.252|
|-----------------------------------------------------------------------------|
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.4246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   7291  Z= 0.158
  Angle     :  0.834  18.985   9882  Z= 0.396
  Chirality :  0.046   0.282   1147
  Planarity :  0.004   0.060   1292
  Dihedral  :  5.393  52.178    995
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 19.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 21.14 %
    Favored  : 76.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.29), residues: 915
  helix:  0.62 (0.20), residues: 687
  sheet:  None (None), residues: 0
  loop :  0.00 (0.48), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  80 
 HIS   0.003   0.001   HIS A  97 
 PHE   0.018   0.002   PHE A 503 
 TYR   0.013   0.001   TYR A 757 
 ARG   0.010   0.000   ARG A 593 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03998 (  479)
  hydrogen bonds       : angle       4.83477 ( 1413)
  covalent geometry    : bond        0.00351 ( 7291)
  covalent geometry    : angle       0.83388 ( 9882)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 133
  time to evaluate  : 0.779 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 TRP cc_start: 0.8503 (t-100) cc_final: 0.7953 (t-100)
REVERT: A  146 MET cc_start: 0.9566 (tmm) cc_final: 0.9228 (tmm)
REVERT: A  239 GLN cc_start: 0.9704 (tt0) cc_final: 0.9350 (tm-30)
REVERT: A  240 ASN cc_start: 0.9435 (OUTLIER) cc_final: 0.8740 (m110)
REVERT: A  281 GLU cc_start: 0.9156 (tp30) cc_final: 0.8514 (tp30)
REVERT: A  282 PHE cc_start: 0.9497 (t80) cc_final: 0.9073 (t80)
REVERT: A  287 CYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8007 (t)
REVERT: A  291 MET cc_start: 0.8741 (mmm) cc_final: 0.8469 (mmm)
REVERT: A  353 MET cc_start: 0.9463 (tpp) cc_final: 0.8785 (tpp)
REVERT: A  354 LEU cc_start: 0.9720 (mm) cc_final: 0.9397 (tp)
REVERT: A  388 MET cc_start: 0.9420 (tpp) cc_final: 0.9039 (tpp)
REVERT: A  436 CYS cc_start: 0.9683 (m) cc_final: 0.9303 (t)
REVERT: A  503 PHE cc_start: 0.9522 (t80) cc_final: 0.8995 (t80)
REVERT: A  513 THR cc_start: 0.9641 (OUTLIER) cc_final: 0.9434 (p)
REVERT: A  529 TYR cc_start: 0.8526 (m-80) cc_final: 0.7679 (m-80)
REVERT: A  568 ILE cc_start: 0.6771 (OUTLIER) cc_final: 0.6363 (mm)
REVERT: A  589 GLN cc_start: 0.9641 (mt0) cc_final: 0.9382 (mp10)
REVERT: A  614 MET cc_start: 0.9162 (tpp) cc_final: 0.8811 (mmt)
REVERT: A  643 PHE cc_start: 0.9464 (t80) cc_final: 0.8991 (t80)
REVERT: A  650 PHE cc_start: 0.9610 (t80) cc_final: 0.9181 (t80)
REVERT: A  714 LEU cc_start: 0.9682 (mt) cc_final: 0.9426 (tp)
REVERT: A  728 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.8600 (t80)
REVERT: B   18 LYS cc_start: 0.8986 (ttmm) cc_final: 0.8623 (ttmm)
REVERT: B   22 LYS cc_start: 0.7062 (mmmm) cc_final: 0.6267 (mppt)
  outliers start: 19
  outliers final: 12
  residues processed: 148
  average time/residue: 0.2061
  time to fit residues: 40.5197
Evaluate side-chains
  141 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 124
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  208 ASN
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  240 ASN
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  255 TYR
Chi-restraints excluded: chain A residue  273 ASP
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  287 CYS
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  448 TYR
Chi-restraints excluded: chain A residue  513 THR
Chi-restraints excluded: chain A residue  568 ILE
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  728 PHE
Chi-restraints excluded: chain A residue  863 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 66 optimal weight:    5.9990
   chunk 48 optimal weight:   10.0000
   chunk 31 optimal weight:   20.0000
   chunk 76 optimal weight:    6.9990
   chunk 69 optimal weight:    0.9990
   chunk 67 optimal weight:    5.9990
   chunk 18 optimal weight:   10.0000
   chunk 6 optimal weight:    9.9990
   chunk 17 optimal weight:   10.0000
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 208 ASN
** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 508 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 = 0.3987 r_free = 0.3987 target = 0.090992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.077105 restraints weight = 57436.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.078622 restraints weight = 26554.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.079512 restraints weight = 15633.442|
|-----------------------------------------------------------------------------|
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.4413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075   7291  Z= 0.156
  Angle     :  0.844  19.035   9882  Z= 0.400
  Chirality :  0.046   0.229   1147
  Planarity :  0.004   0.058   1292
  Dihedral  :  5.387  51.829    995
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 19.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 22.41 %
    Favored  : 74.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.29), residues: 915
  helix:  0.60 (0.20), residues: 694
  sheet:  None (None), residues: 0
  loop : -0.04 (0.49), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  80 
 HIS   0.003   0.001   HIS B  15 
 PHE   0.019   0.002   PHE A 503 
 TYR   0.013   0.001   TYR A 248 
 ARG   0.013   0.001   ARG A 593 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03907 (  479)
  hydrogen bonds       : angle       4.84467 ( 1413)
  covalent geometry    : bond        0.00349 ( 7291)
  covalent geometry    : angle       0.84393 ( 9882)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 130
  time to evaluate  : 0.876 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 TRP cc_start: 0.8562 (t-100) cc_final: 0.7997 (t-100)
REVERT: A  146 MET cc_start: 0.9566 (tmm) cc_final: 0.9218 (tmm)
REVERT: A  181 MET cc_start: 0.7694 (tpp) cc_final: 0.7078 (tpp)
REVERT: A  239 GLN cc_start: 0.9711 (tt0) cc_final: 0.9349 (tm-30)
REVERT: A  240 ASN cc_start: 0.9445 (OUTLIER) cc_final: 0.8736 (m110)
REVERT: A  281 GLU cc_start: 0.9166 (tp30) cc_final: 0.8512 (tp30)
REVERT: A  282 PHE cc_start: 0.9514 (t80) cc_final: 0.9073 (t80)
REVERT: A  287 CYS cc_start: 0.9214 (OUTLIER) cc_final: 0.7850 (t)
REVERT: A  291 MET cc_start: 0.8771 (mmm) cc_final: 0.8504 (mmm)
REVERT: A  354 LEU cc_start: 0.9748 (mm) cc_final: 0.9426 (tp)
REVERT: A  388 MET cc_start: 0.9411 (tpp) cc_final: 0.9023 (tpp)
REVERT: A  436 CYS cc_start: 0.9714 (m) cc_final: 0.9362 (t)
REVERT: A  472 TRP cc_start: 0.8855 (OUTLIER) cc_final: 0.8030 (m-90)
REVERT: A  503 PHE cc_start: 0.9518 (t80) cc_final: 0.9004 (t80)
REVERT: A  568 ILE cc_start: 0.6302 (OUTLIER) cc_final: 0.5842 (mm)
REVERT: A  589 GLN cc_start: 0.9638 (mt0) cc_final: 0.9411 (mp10)
REVERT: A  614 MET cc_start: 0.9170 (tpp) cc_final: 0.8796 (mmt)
REVERT: A  643 PHE cc_start: 0.9450 (t80) cc_final: 0.9002 (t80)
REVERT: A  650 PHE cc_start: 0.9607 (t80) cc_final: 0.9163 (t80)
REVERT: A  714 LEU cc_start: 0.9684 (mt) cc_final: 0.9448 (tp)
REVERT: B   18 LYS cc_start: 0.8986 (ttmm) cc_final: 0.8648 (ttmm)
REVERT: B   22 LYS cc_start: 0.7093 (mmmm) cc_final: 0.6684 (mppt)
REVERT: B   26 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8448 (pp20)
REVERT: B   30 ARG cc_start: 0.9598 (mtp85) cc_final: 0.9286 (ttm110)
  outliers start: 23
  outliers final: 15
  residues processed: 147
  average time/residue: 0.2021
  time to fit residues: 39.3237
Evaluate side-chains
  142 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  208 ASN
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  240 ASN
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  255 TYR
Chi-restraints excluded: chain A residue  273 ASP
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  287 CYS
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  448 TYR
Chi-restraints excluded: chain A residue  472 TRP
Chi-restraints excluded: chain A residue  568 ILE
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  863 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 4 optimal weight:   40.0000
   chunk 65 optimal weight:    6.9990
   chunk 33 optimal weight:    8.9990
   chunk 32 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 25 optimal weight:    9.9990
   chunk 9 optimal weight:    6.9990
   chunk 43 optimal weight:    1.9990
   chunk 61 optimal weight:    7.9990
   chunk 47 optimal weight:    2.9990
   overall best weight:    1.7188

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

Flipped N/Q/H residues before XYZ refinement:
A 208 ASN
A 401 GLN
** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 744 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.080865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.073682 restraints weight = 54718.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.075061 restraints weight = 24469.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.075850 restraints weight = 13564.367|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.4544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   7291  Z= 0.143
  Angle     :  0.885  19.146   9882  Z= 0.408
  Chirality :  0.048   0.279   1147
  Planarity :  0.004   0.059   1292
  Dihedral  :  5.603  61.777    995
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 19.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 23.92 %
    Favored  : 73.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.29), residues: 915
  helix:  0.56 (0.20), residues: 693
  sheet:  None (None), residues: 0
  loop : -0.05 (0.48), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 430 
 HIS   0.002   0.001   HIS A  97 
 PHE   0.017   0.001   PHE A 503 
 TYR   0.014   0.001   TYR A 248 
 ARG   0.012   0.000   ARG A 593 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03816 (  479)
  hydrogen bonds       : angle       4.78175 ( 1413)
  covalent geometry    : bond        0.00327 ( 7291)
  covalent geometry    : angle       0.88516 ( 9882)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 130
  time to evaluate  : 0.808 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 TRP cc_start: 0.8478 (t-100) cc_final: 0.7921 (t-100)
REVERT: A  146 MET cc_start: 0.9569 (tmm) cc_final: 0.9232 (tmm)
REVERT: A  181 MET cc_start: 0.7783 (tpp) cc_final: 0.7241 (tpp)
REVERT: A  239 GLN cc_start: 0.9701 (tt0) cc_final: 0.9347 (tm-30)
REVERT: A  240 ASN cc_start: 0.9465 (OUTLIER) cc_final: 0.8737 (m110)
REVERT: A  281 GLU cc_start: 0.9100 (tp30) cc_final: 0.8446 (tp30)
REVERT: A  282 PHE cc_start: 0.9481 (t80) cc_final: 0.9014 (t80)
REVERT: A  287 CYS cc_start: 0.9203 (OUTLIER) cc_final: 0.7763 (t)
REVERT: A  291 MET cc_start: 0.8750 (mmm) cc_final: 0.8458 (mmm)
REVERT: A  353 MET cc_start: 0.9359 (tpp) cc_final: 0.8709 (tpt)
REVERT: A  354 LEU cc_start: 0.9733 (mm) cc_final: 0.9347 (tp)
REVERT: A  388 MET cc_start: 0.9414 (tpp) cc_final: 0.9038 (tpp)
REVERT: A  436 CYS cc_start: 0.9721 (m) cc_final: 0.9343 (t)
REVERT: A  472 TRP cc_start: 0.8846 (OUTLIER) cc_final: 0.8039 (m-90)
REVERT: A  503 PHE cc_start: 0.9530 (t80) cc_final: 0.9061 (t80)
REVERT: A  568 ILE cc_start: 0.6389 (OUTLIER) cc_final: 0.5977 (mm)
REVERT: A  614 MET cc_start: 0.9163 (tpp) cc_final: 0.8781 (mmt)
REVERT: A  643 PHE cc_start: 0.9451 (t80) cc_final: 0.9005 (t80)
REVERT: A  650 PHE cc_start: 0.9622 (t80) cc_final: 0.9156 (t80)
REVERT: A  714 LEU cc_start: 0.9695 (mt) cc_final: 0.9442 (tp)
REVERT: B   18 LYS cc_start: 0.8923 (ttmm) cc_final: 0.8507 (ttmm)
REVERT: B   22 LYS cc_start: 0.7052 (mmmm) cc_final: 0.6774 (mppt)
REVERT: B   26 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8172 (pp20)
REVERT: B   27 MET cc_start: 0.9524 (mmm) cc_final: 0.9036 (mmm)
REVERT: B   29 ARG cc_start: 0.9599 (ttp80) cc_final: 0.9269 (tmm-80)
REVERT: B   30 ARG cc_start: 0.9604 (mtp85) cc_final: 0.9349 (ttm-80)
  outliers start: 20
  outliers final: 14
  residues processed: 145
  average time/residue: 0.2119
  time to fit residues: 40.4038
Evaluate side-chains
  140 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 122
  time to evaluate  : 0.866 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  208 ASN
Chi-restraints excluded: chain A residue  240 ASN
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  255 TYR
Chi-restraints excluded: chain A residue  273 ASP
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  287 CYS
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  401 GLN
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  448 TYR
Chi-restraints excluded: chain A residue  472 TRP
Chi-restraints excluded: chain A residue  568 ILE
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  863 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 68 optimal weight:    9.9990
   chunk 79 optimal weight:    3.9990
   chunk 38 optimal weight:    6.9990
   chunk 16 optimal weight:    7.9990
   chunk 40 optimal weight:    7.9990
   chunk 10 optimal weight:    8.9990
   chunk 41 optimal weight:    0.6980
   chunk 62 optimal weight:    0.0070
   chunk 82 optimal weight:   20.0000
   chunk 65 optimal weight:    1.9990
   chunk 0 optimal weight:   50.0000
   overall best weight:    2.7404

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

Flipped N/Q/H residues before XYZ refinement:
A 401 GLN
** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 590 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.052602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.039530 restraints weight = 57812.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.040444 restraints weight = 40993.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.041089 restraints weight = 32025.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.4699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   7291  Z= 0.156
  Angle     :  0.921  20.012   9882  Z= 0.430
  Chirality :  0.048   0.242   1147
  Planarity :  0.004   0.064   1292
  Dihedral  :  5.040  51.583    992
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 20.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 25.19 %
    Favored  : 72.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.29), residues: 915
  helix:  0.58 (0.20), residues: 692
  sheet:  None (None), residues: 0
  loop : -0.08 (0.48), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 430 
 HIS   0.002   0.001   HIS A  97 
 PHE   0.017   0.001   PHE A 503 
 TYR   0.024   0.001   TYR A 664 
 ARG   0.011   0.001   ARG A 593 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03842 (  479)
  hydrogen bonds       : angle       4.88683 ( 1413)
  covalent geometry    : bond        0.00350 ( 7291)
  covalent geometry    : angle       0.92128 ( 9882)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 126
  time to evaluate  : 0.841 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 TRP cc_start: 0.8709 (t-100) cc_final: 0.8145 (t-100)
REVERT: A  239 GLN cc_start: 0.9704 (tt0) cc_final: 0.9348 (tm-30)
REVERT: A  240 ASN cc_start: 0.9447 (OUTLIER) cc_final: 0.8729 (m110)
REVERT: A  281 GLU cc_start: 0.9135 (tp30) cc_final: 0.8436 (tp30)
REVERT: A  282 PHE cc_start: 0.9462 (t80) cc_final: 0.8994 (t80)
REVERT: A  287 CYS cc_start: 0.9248 (OUTLIER) cc_final: 0.7941 (t)
REVERT: A  291 MET cc_start: 0.8859 (mmm) cc_final: 0.8611 (mmm)
REVERT: A  353 MET cc_start: 0.9196 (tpp) cc_final: 0.8633 (tpt)
REVERT: A  354 LEU cc_start: 0.9736 (mm) cc_final: 0.9347 (tp)
REVERT: A  388 MET cc_start: 0.9423 (tpp) cc_final: 0.9029 (tpp)
REVERT: A  436 CYS cc_start: 0.9750 (m) cc_final: 0.9314 (t)
REVERT: A  472 TRP cc_start: 0.8837 (OUTLIER) cc_final: 0.8036 (m-90)
REVERT: A  503 PHE cc_start: 0.9682 (t80) cc_final: 0.9278 (t80)
REVERT: A  568 ILE cc_start: 0.6619 (OUTLIER) cc_final: 0.6180 (mm)
REVERT: A  614 MET cc_start: 0.9258 (tpp) cc_final: 0.8890 (mmt)
REVERT: A  643 PHE cc_start: 0.9405 (t80) cc_final: 0.9017 (t80)
REVERT: A  650 PHE cc_start: 0.9607 (t80) cc_final: 0.9166 (t80)
REVERT: A  714 LEU cc_start: 0.9697 (mt) cc_final: 0.9415 (tp)
REVERT: B   18 LYS cc_start: 0.8982 (ttmm) cc_final: 0.8522 (ttmm)
REVERT: B   26 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8129 (pp20)
REVERT: B   27 MET cc_start: 0.9591 (mmm) cc_final: 0.9183 (mmm)
REVERT: B   30 ARG cc_start: 0.9653 (mtp85) cc_final: 0.9411 (ttm-80)
  outliers start: 18
  outliers final: 13
  residues processed: 139
  average time/residue: 0.2120
  time to fit residues: 38.8412
Evaluate side-chains
  137 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  240 ASN
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  255 TYR
Chi-restraints excluded: chain A residue  273 ASP
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  287 CYS
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  401 GLN
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  448 TYR
Chi-restraints excluded: chain A residue  472 TRP
Chi-restraints excluded: chain A residue  568 ILE
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  863 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 52 optimal weight:    9.9990
   chunk 21 optimal weight:    8.9990
   chunk 48 optimal weight:   10.0000
   chunk 16 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9990
   chunk 66 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 28 optimal weight:   10.0000
   chunk 84 optimal weight:   10.0000
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 208 ASN
A 401 GLN
** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 508 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 = 0.3418 r_free = 0.3418 target = 0.053546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.040168 restraints weight = 56572.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.041115 restraints weight = 40328.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.041784 restraints weight = 31485.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.4784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   7291  Z= 0.150
  Angle     :  0.986  20.719   9882  Z= 0.454
  Chirality :  0.051   0.281   1147
  Planarity :  0.004   0.066   1292
  Dihedral  :  5.070  51.484    992
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 18.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 25.44 %
    Favored  : 72.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.29), residues: 915
  helix:  0.48 (0.20), residues: 693
  sheet:  None (None), residues: 0
  loop : -0.04 (0.48), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 430 
 HIS   0.002   0.000   HIS A  97 
 PHE   0.017   0.001   PHE A 503 
 TYR   0.014   0.001   TYR A 248 
 ARG   0.009   0.000   ARG A 593 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03919 (  479)
  hydrogen bonds       : angle       4.88868 ( 1413)
  covalent geometry    : bond        0.00333 ( 7291)
  covalent geometry    : angle       0.98637 ( 9882)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 TRP cc_start: 0.8663 (t-100) cc_final: 0.8080 (t-100)
REVERT: A  181 MET cc_start: 0.7784 (tpp) cc_final: 0.7167 (tpp)
REVERT: A  239 GLN cc_start: 0.9678 (tt0) cc_final: 0.9316 (tm-30)
REVERT: A  240 ASN cc_start: 0.9510 (OUTLIER) cc_final: 0.8849 (m110)
REVERT: A  282 PHE cc_start: 0.9451 (t80) cc_final: 0.8953 (t80)
REVERT: A  285 ASN cc_start: 0.9344 (m-40) cc_final: 0.9112 (m110)
REVERT: A  287 CYS cc_start: 0.9233 (OUTLIER) cc_final: 0.7721 (t)
REVERT: A  291 MET cc_start: 0.8856 (mmm) cc_final: 0.8584 (mmm)
REVERT: A  353 MET cc_start: 0.9259 (tpp) cc_final: 0.8638 (tpt)
REVERT: A  354 LEU cc_start: 0.9739 (mm) cc_final: 0.9325 (tp)
REVERT: A  388 MET cc_start: 0.9437 (tpp) cc_final: 0.9121 (tpp)
REVERT: A  401 GLN cc_start: 0.9747 (OUTLIER) cc_final: 0.9431 (mp10)
REVERT: A  436 CYS cc_start: 0.9761 (m) cc_final: 0.9285 (t)
REVERT: A  503 PHE cc_start: 0.9700 (t80) cc_final: 0.9288 (t80)
REVERT: A  568 ILE cc_start: 0.6634 (OUTLIER) cc_final: 0.6181 (mm)
REVERT: A  614 MET cc_start: 0.9271 (tpp) cc_final: 0.8915 (mmt)
REVERT: A  643 PHE cc_start: 0.9409 (t80) cc_final: 0.9008 (t80)
REVERT: A  650 PHE cc_start: 0.9638 (t80) cc_final: 0.9183 (t80)
REVERT: A  714 LEU cc_start: 0.9702 (mt) cc_final: 0.9364 (tp)
REVERT: B   16 ARG cc_start: 0.9348 (mmm-85) cc_final: 0.9139 (mmm-85)
REVERT: B   18 LYS cc_start: 0.8898 (ttmm) cc_final: 0.8501 (ttmm)
REVERT: B   26 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8166 (pp20)
REVERT: B   27 MET cc_start: 0.9599 (mmm) cc_final: 0.9187 (mmm)
REVERT: B   29 ARG cc_start: 0.9618 (ttp80) cc_final: 0.9327 (tmm-80)
REVERT: B   30 ARG cc_start: 0.9669 (mtp85) cc_final: 0.9382 (ttm-80)
  outliers start: 18
  outliers final: 12
  residues processed: 143
  average time/residue: 0.2037
  time to fit residues: 38.4688
Evaluate side-chains
  142 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 126
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  208 ASN
Chi-restraints excluded: chain A residue  240 ASN
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  255 TYR
Chi-restraints excluded: chain A residue  273 ASP
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  287 CYS
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  401 GLN
Chi-restraints excluded: chain A residue  448 TYR
Chi-restraints excluded: chain A residue  568 ILE
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  863 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 48 optimal weight:    7.9990
   chunk 79 optimal weight:    7.9990
   chunk 75 optimal weight:    6.9990
   chunk 66 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   chunk 7 optimal weight:    9.9990
   chunk 74 optimal weight:   30.0000
   chunk 23 optimal weight:    1.9990
   chunk 42 optimal weight:   10.0000
   chunk 46 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 508 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 = 0.3416 r_free = 0.3416 target = 0.053131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.039980 restraints weight = 57432.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.040907 restraints weight = 41179.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.041588 restraints weight = 32292.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.4858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.194   7291  Z= 0.282
  Angle     :  1.339  59.198   9882  Z= 0.746
  Chirality :  0.061   0.866   1147
  Planarity :  0.007   0.183   1292
  Dihedral  :  5.255  51.499    992
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 23.44
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.84 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 26.20 %
    Favored  : 71.77 %
  Cbeta Deviations :  0.23 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.29), residues: 915
  helix:  0.46 (0.20), residues: 695
  sheet:  None (None), residues: 0
  loop :  0.07 (0.49), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 472 
 HIS   0.002   0.000   HIS A  97 
 PHE   0.015   0.001   PHE A 503 
 TYR   0.013   0.001   TYR A 248 
 ARG   0.027   0.001   ARG A 593 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04022 (  479)
  hydrogen bonds       : angle       4.93659 ( 1413)
  covalent geometry    : bond        0.00640 ( 7291)
  covalent geometry    : angle       1.33878 ( 9882)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2874.78 seconds
wall clock time: 50 minutes 26.92 seconds (3026.92 seconds total)