Starting phenix.real_space_refine
on Wed Feb  4 00:49:44 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rqi_54175/02_2026/9rqi_54175.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rqi_54175/02_2026/9rqi_54175.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rqi_54175/02_2026/9rqi_54175.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rqi_54175/02_2026/9rqi_54175.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rqi_54175/02_2026/9rqi_54175.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rqi_54175/02_2026/9rqi_54175.map"
  }
  resolution = 2.76
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.010
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      32      5.16       5
     C    4974      2.51       5
     N    1375      2.21       5
     O    1518      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7899
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4774
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 582, 4774
          Classifications: {'peptide': 582}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 557}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1187
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 151, 1187
          Classifications: {'peptide': 151}
          Link IDs: {'PTRANS': 8, 'TRANS': 142}
    Chain: "C"
      Number of atoms: 1938
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1938
          Classifications: {'peptide': 254}
          Link IDs: {'PTRANS': 13, 'TRANS': 240}
          Chain breaks: 2
  Time building chain proxies: 1.92, per 1000 atoms: 0.24
  Number of scatterers: 7899
  At special positions: 0
  Unit cell: (109.52, 86.58, 101.38, 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      32     16.00
     O    1518      8.00
     N    1375      7.00
     C    4974      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.74
  Conformation dependent library (CDL) restraints added in 310.8 milliseconds
  

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1840

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 8 sheets defined
      9.9% alpha, 45.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 295 through 302
      removed outlier: 3.739A  pdb=" N   GLU A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ASP A 300 " --> pdb=" O   LYS A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 464 through 470
    Processing helix  chain 'A' and resid 537 through 542
      removed outlier: 3.788A  pdb=" N   PHE A 541 " --> pdb=" O   SER A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 668
    Processing helix  chain 'A' and resid 669 through 673
    Processing helix  chain 'B' and resid 30 through 33
    Processing helix  chain 'B' and resid 45 through 58
      removed outlier: 3.625A  pdb=" N   ASN B  58 " --> pdb=" O   GLN B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 158
      removed outlier: 3.634A  pdb=" N   LYS B 158 " --> pdb=" O   GLN B 154 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 169
    Processing sheet with id=AA1, first strand: chain 'A' and resid 198 through 207
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 198 through 207
    current: chain 'A' and resid 240 through 244
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 240 through 244
    current: chain 'A' and resid 255 through 264
      removed outlier: 3.534A  pdb=" N   ASN A 269 " --> pdb=" O   MET A 264 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLY A 285 " --> pdb=" O   TYR A 278 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   VAL A 329 " --> pdb=" O   HIS A 317 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 325 through 334
    current: chain 'A' and resid 354 through 364
      removed outlier: 4.293A  pdb=" N   ALA A 355 " --> pdb=" O   GLN A 378 " (cutoff:3.500A)
      removed outlier: 7.222A  pdb=" N   LYS A 375 " --> pdb=" O   GLU A 391 " (cutoff:3.500A)
      removed outlier: 4.747A  pdb=" N   GLU A 391 " --> pdb=" O   LYS A 375 " (cutoff:3.500A)
      removed outlier: 8.491A  pdb=" N   PHE A 377 " --> pdb=" O   SER A 389 " (cutoff:3.500A)
      removed outlier: 9.539A  pdb=" N   SER A 389 " --> pdb=" O   PHE A 377 " (cutoff:3.500A)
      removed outlier: 5.658A  pdb=" N   ALA A 390 " --> pdb=" O   VAL A 418 " (cutoff:3.500A)
      removed outlier: 7.338A  pdb=" N   VAL A 418 " --> pdb=" O   ALA A 390 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ASP A 402 " --> pdb=" O   PHE A 406 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   PHE A 406 " --> pdb=" O   ASP A 402 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   VAL A 478 " --> pdb=" O   TYR A 458 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 477 through 491
    current: chain 'A' and resid 504 through 517
      removed outlier: 7.652A  pdb=" N   ASN A 556 " --> pdb=" O   TYR A 584 " (cutoff:3.500A)
      removed outlier: 4.978A  pdb=" N   TYR A 584 " --> pdb=" O   ASN A 556 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   VAL A 558 " --> pdb=" O   ILE A 582 " (cutoff:3.500A)
      removed outlier: 4.846A  pdb=" N   ILE A 582 " --> pdb=" O   VAL A 558 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   THR A 560 " --> pdb=" O   GLY A 580 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   GLY A 580 " --> pdb=" O   THR A 560 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   VAL A 562 " --> pdb=" O   SER A 578 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   SER A 578 " --> pdb=" O   VAL A 562 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   SER A 564 " --> pdb=" O   ASN A 576 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   ASN A 576 " --> pdb=" O   SER A 564 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   ILE A 566 " --> pdb=" O   ARG A 574 " (cutoff:3.500A)
      removed outlier: 8.220A  pdb=" N   ARG A 574 " --> pdb=" O   TRP A 614 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   TRP A 614 " --> pdb=" O   ARG A 574 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   ASN A 576 " --> pdb=" O   THR A 612 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   THR A 612 " --> pdb=" O   ASN A 576 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   SER A 578 " --> pdb=" O   GLY A 610 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   GLY A 610 " --> pdb=" O   SER A 578 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   GLY A 580 " --> pdb=" O   TRP A 608 " (cutoff:3.500A)
      removed outlier: 4.532A  pdb=" N   TRP A 608 " --> pdb=" O   GLY A 580 " (cutoff:3.500A)
      removed outlier: 7.433A  pdb=" N   ILE A 582 " --> pdb=" O   LEU A 606 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LEU A 606 " --> pdb=" O   ILE A 582 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 620 through 623
    current: chain 'A' and resid 634 through 645
      removed outlier: 3.677A  pdb=" N   LEU A 651 " --> pdb=" O   SER A 690 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   GLY A 686 " --> pdb=" O   ASN A 655 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   SER A 698 " --> pdb=" O   VAL A 719 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   VAL A 719 " --> pdb=" O   SER A 698 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   VAL A 700 " --> pdb=" O   LEU A 717 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   LEU A 717 " --> pdb=" O   VAL A 700 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   ALA A 702 " --> pdb=" O   SER A 715 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   SER A 715 " --> pdb=" O   ALA A 702 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   TYR A 704 " --> pdb=" O   ALA A 713 " (cutoff:3.500A)
      removed outlier: 8.727A  pdb=" N   ALA A 713 " --> pdb=" O   LEU A 736 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   LEU A 736 " --> pdb=" O   ALA A 713 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 530 through 532
      removed outlier: 3.700A  pdb=" N   SER A 531 " --> pdb=" O   GLY A 547 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 63
      removed outlier: 3.682A  pdb=" N   MET B  36 " --> pdb=" O   GLU B  61 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   LEU B  38 " --> pdb=" O   LEU B  63 " (cutoff:3.500A)
      removed outlier: 8.299A  pdb=" N   LEU B  75 " --> pdb=" O   VAL B  35 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   ILE B  37 " --> pdb=" O   LEU B  75 " (cutoff:3.500A)
      removed outlier: 7.449A  pdb=" N   LEU B  77 " --> pdb=" O   ILE B  37 " (cutoff:3.500A)
      removed outlier: 7.135A  pdb=" N   ASP B  39 " --> pdb=" O   LEU B  77 " (cutoff:3.500A)
      removed outlier: 9.252A  pdb=" N   LYS B  79 " --> pdb=" O   ASP B  39 " (cutoff:3.500A)
      removed outlier: 5.652A  pdb=" N   LEU B  75 " --> pdb=" O   LEU B 109 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   LEU B 109 " --> pdb=" O   LEU B  75 " (cutoff:3.500A)
      removed outlier: 5.229A  pdb=" N   LEU B  77 " --> pdb=" O   THR B 107 " (cutoff:3.500A)
      removed outlier: 6.222A  pdb=" N   THR B 107 " --> pdb=" O   LEU B  77 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   LYS B  79 " --> pdb=" O   ASN B 105 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   GLU B  97 " --> pdb=" O   ALA B  87 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   VAL B  89 " --> pdb=" O   THR B  95 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   THR B  95 " --> pdb=" O   VAL B  89 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 26 through 34
      removed outlier: 6.866A  pdb=" N   ILE C 111 " --> pdb=" O   CYS C  28 " (cutoff:3.500A)
      removed outlier: 4.811A  pdb=" N   SER C  30 " --> pdb=" O   GLY C 109 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   GLY C 109 " --> pdb=" O   SER C  30 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   ASN C  32 " --> pdb=" O   TRP C 107 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   TRP C 107 " --> pdb=" O   ASN C  32 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   ALA C 108 " --> pdb=" O   THR C  58 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 40 through 44
      removed outlier: 7.116A  pdb=" N   GLY C  89 " --> pdb=" O   ARG C  84 " (cutoff:3.500A)
      removed outlier: 5.129A  pdb=" N   ARG C  84 " --> pdb=" O   GLY C  89 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   THR C  91 " --> pdb=" O   VAL C  82 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   VAL C  82 " --> pdb=" O   THR C  91 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   ARG C  93 " --> pdb=" O   THR C  80 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 233 through 234
      removed outlier: 4.590A  pdb=" N   LYS C 233 " --> pdb=" O   CYS C 144 " (cutoff:3.500A)
      removed outlier: 5.787A  pdb=" N   CYS C 144 " --> pdb=" O   ASN C 207 " (cutoff:3.500A)
      removed outlier: 7.138A  pdb=" N   ASN C 207 " --> pdb=" O   CYS C 144 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   LEU C 315 " --> pdb=" O   GLN C 256 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ARG C 239 " --> pdb=" O   VAL C 316 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 155 through 157
    Processing sheet with id=AA8, first strand: chain 'C' and resid 248 through 249
      removed outlier: 3.645A  pdb=" N   ALA C 288 " --> pdb=" O   GLY C 277 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   MET C 275 " --> pdb=" O   ASN C 290 " (cutoff:3.500A)
      removed outlier: 5.001A  pdb=" N   VAL C 292 " --> pdb=" O   VAL C 273 " (cutoff:3.500A)
      removed outlier: 7.560A  pdb=" N   VAL C 273 " --> pdb=" O   VAL C 292 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   GLY C 294 " --> pdb=" O   ASN C 271 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   ASN C 271 " --> pdb=" O   GLY C 294 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   GLY C 261 " --> pdb=" O   ASN C 276 " (cutoff:3.500A)

    306 hydrogen bonds defined for protein.
    861 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.40

  Time building geometry restraints manager: 0.95 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2635
        1.34 -     1.46: 1806
        1.46 -     1.58: 3582
        1.58 -     1.69: 0
        1.69 -     1.81: 59
  Bond restraints: 8082
  Sorted by residual:
  bond pdb=" N   ILE A 210 "
       pdb=" CA  ILE A 210 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 1.20e-02 6.94e+03 8.64e+00
  bond pdb=" N   PHE A 211 "
       pdb=" CA  PHE A 211 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.035 1.19e-02 7.06e+03 8.62e+00
  bond pdb=" N   VAL A 208 "
       pdb=" CA  VAL A 208 "
    ideal  model  delta    sigma   weight residual
    1.461  1.492 -0.031 1.23e-02 6.61e+03 6.38e+00
  bond pdb=" N   GLY A 206 "
       pdb=" CA  GLY A 206 "
    ideal  model  delta    sigma   weight residual
    1.443  1.472 -0.029 1.37e-02 5.33e+03 4.51e+00
  bond pdb=" N   PRO A 209 "
       pdb=" CD  PRO A 209 "
    ideal  model  delta    sigma   weight residual
    1.473  1.450  0.023 1.40e-02 5.10e+03 2.63e+00
  ... (remaining 8077 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.50: 10768
        1.50 -     2.99: 176
        2.99 -     4.49: 32
        4.49 -     5.99: 5
        5.99 -     7.49: 2
  Bond angle restraints: 10983
  Sorted by residual:
  angle pdb=" C   ALA A 694 "
        pdb=" CA  ALA A 694 "
        pdb=" CB  ALA A 694 "
      ideal   model   delta    sigma   weight residual
     116.34  110.69    5.65 1.40e+00 5.10e-01 1.63e+01
  angle pdb=" C   THR A 769 "
        pdb=" N   GLN A 770 "
        pdb=" CA  GLN A 770 "
      ideal   model   delta    sigma   weight residual
     121.54  127.99   -6.45 1.91e+00 2.74e-01 1.14e+01
  angle pdb=" C   PHE A 211 "
        pdb=" CA  PHE A 211 "
        pdb=" CB  PHE A 211 "
      ideal   model   delta    sigma   weight residual
     109.37  115.06   -5.69 1.83e+00 2.99e-01 9.65e+00
  angle pdb=" CA  LYS B  70 "
        pdb=" CB  LYS B  70 "
        pdb=" CG  LYS B  70 "
      ideal   model   delta    sigma   weight residual
     114.10  119.58   -5.48 2.00e+00 2.50e-01 7.50e+00
  angle pdb=" C   ASP A 592 "
        pdb=" N   ASP A 593 "
        pdb=" CA  ASP A 593 "
      ideal   model   delta    sigma   weight residual
     121.54  126.12   -4.58 1.91e+00 2.74e-01 5.76e+00
  ... (remaining 10978 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 4131
       17.97 -    35.93: 508
       35.93 -    53.90: 126
       53.90 -    71.86: 27
       71.86 -    89.83: 11
  Dihedral angle restraints: 4803
    sinusoidal: 1916
      harmonic: 2887
  Sorted by residual:
  dihedral pdb=" CB  GLU A 197 "
           pdb=" CG  GLU A 197 "
           pdb=" CD  GLU A 197 "
           pdb=" OE1 GLU A 197 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.83   89.83     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CG  ARG A 589 "
           pdb=" CD  ARG A 589 "
           pdb=" NE  ARG A 589 "
           pdb=" CZ  ARG A 589 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -134.61   44.61     2      1.50e+01 4.44e-03 1.05e+01
  dihedral pdb=" CA  ASP A 706 "
           pdb=" CB  ASP A 706 "
           pdb=" CG  ASP A 706 "
           pdb=" OD1 ASP A 706 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -85.25   55.25     1      2.00e+01 2.50e-03 1.03e+01
  ... (remaining 4800 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 821
       0.039 -    0.077: 225
       0.077 -    0.116: 105
       0.116 -    0.154: 21
       0.154 -    0.193: 2
  Chirality restraints: 1174
  Sorted by residual:
  chirality pdb=" CA  ILE A 210 "
            pdb=" N   ILE A 210 "
            pdb=" C   ILE A 210 "
            pdb=" CB  ILE A 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.19 2.00e-01 2.50e+01 9.29e-01
  chirality pdb=" CA  VAL A 208 "
            pdb=" N   VAL A 208 "
            pdb=" C   VAL A 208 "
            pdb=" CB  VAL A 208 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.18 2.00e-01 2.50e+01 8.36e-01
  chirality pdb=" CB  VAL A 208 "
            pdb=" CA  VAL A 208 "
            pdb=" CG1 VAL A 208 "
            pdb=" CG2 VAL A 208 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.49   -0.14 2.00e-01 2.50e+01 4.91e-01
  ... (remaining 1171 not shown)

  Planarity restraints: 1446
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 783 "    0.009 2.00e-02 2.50e+03   1.87e-02 3.51e+00
        pdb=" C   THR A 783 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   THR A 783 "    0.012 2.00e-02 2.50e+03
        pdb=" N   LEU A 784 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 391 "    0.024 5.00e-02 4.00e+02   3.65e-02 2.13e+00
        pdb=" N   PRO A 392 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 392 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 392 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 252 "   -0.021 5.00e-02 4.00e+02   3.22e-02 1.66e+00
        pdb=" N   PRO A 253 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 253 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 253 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 1443 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1667
        2.78 -     3.31: 6559
        3.31 -     3.84: 12575
        3.84 -     4.37: 15040
        4.37 -     4.90: 27816
  Nonbonded interactions: 63657
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU C  65 "
            pdb=" OH  TYR C 296 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" OD2 ASP A 352 "
            pdb=" OG  SER A 387 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" NE2 GLN B 131 "
            pdb=" OG1 THR C  70 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" OH  TYR A 628 "
            pdb=" OD1 ASP A 633 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" N   GLU A 587 "
            pdb=" OE1 GLU A 587 "
     model   vdw
     2.280 3.120
  ... (remaining 63652 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             7.140
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.440
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
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      :  0.004   0.035   8082  Z= 0.176
  Angle     :  0.501   7.487  10983  Z= 0.275
  Chirality :  0.045   0.193   1174
  Planarity :  0.003   0.036   1446
  Dihedral  : 16.962  89.828   2963
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 27.57 %
    Favored  : 70.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.35 (0.27), residues: 975
  helix:  1.12 (0.58), residues: 89
  sheet:  0.24 (0.24), residues: 502
  loop : -1.13 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  23 
 TYR   0.022   0.001   TYR B 148 
 PHE   0.007   0.001   PHE A 211 
 TRP   0.004   0.001   TRP C 168 
 HIS   0.003   0.001   HIS A 745 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 8082)
  covalent geometry    : angle       0.50148 (10983)
  hydrogen bonds       : bond        0.20156 (  306)
  hydrogen bonds       : angle       8.69043 (  861)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.326 
Fit side-chains
REVERT: A  225 ARG cc_start: 0.7979 (ttm-80) cc_final: 0.7774 (ptm160)
REVERT: A  587 GLU cc_start: 0.7721 (mp0) cc_final: 0.7495 (tt0)
REVERT: B  103 THR cc_start: 0.8760 (t) cc_final: 0.8504 (p)
REVERT: B  121 LYS cc_start: 0.8705 (ttmt) cc_final: 0.8367 (ttmt)
  outliers start: 13
  outliers final: 6
  residues processed: 90
  average time/residue: 0.6312
  time to fit residues: 60.0154
Evaluate side-chains
  77 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 71
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  401 ASN
Chi-restraints excluded: chain A residue  471 THR
Chi-restraints excluded: chain A residue  783 THR
Chi-restraints excluded: chain B residue   40 SER
Chi-restraints excluded: chain C residue   80 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.3980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
C  69 GLN
C 186 ASN
C 208 ASN
C 232 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.090708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.069054 restraints weight = 13233.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.2820 rms_B_bonded: 2.79
r_work: 0.2705 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2578 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.0931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8082  Z= 0.140
  Angle     :  0.498   6.226  10983  Z= 0.267
  Chirality :  0.046   0.138   1174
  Planarity :  0.004   0.040   1446
  Dihedral  :  4.478  58.024   1121
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 24.42 %
    Favored  : 72.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.34 (0.27), residues: 975
  helix:  1.39 (0.57), residues: 91
  sheet:  0.29 (0.24), residues: 501
  loop : -1.29 (0.30), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 480 
 TYR   0.017   0.001   TYR A 278 
 PHE   0.006   0.001   PHE A 417 
 TRP   0.014   0.001   TRP A 465 
 HIS   0.002   0.001   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 8082)
  covalent geometry    : angle       0.49831 (10983)
  hydrogen bonds       : bond        0.03868 (  306)
  hydrogen bonds       : angle       5.88384 (  861)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 76
  time to evaluate  : 0.328 
Fit side-chains
REVERT: A  225 ARG cc_start: 0.7955 (ttm-80) cc_final: 0.7747 (ptm160)
REVERT: A  587 GLU cc_start: 0.7792 (mp0) cc_final: 0.7488 (tt0)
REVERT: A  674 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8518 (p)
REVERT: B   62 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8374 (mm)
REVERT: B  121 LYS cc_start: 0.8637 (ttmt) cc_final: 0.8355 (ttmt)
REVERT: C  148 LYS cc_start: 0.7052 (ttmm) cc_final: 0.6698 (ttpp)
  outliers start: 28
  outliers final: 8
  residues processed: 95
  average time/residue: 0.5347
  time to fit residues: 54.0242
Evaluate side-chains
  80 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  452 LYS
Chi-restraints excluded: chain A residue  535 SER
Chi-restraints excluded: chain A residue  611 ASP
Chi-restraints excluded: chain A residue  674 THR
Chi-restraints excluded: chain A residue  783 THR
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   81 SER
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  198 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 91 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 45 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 79 optimal weight:    5.9990
   chunk 63 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 52 optimal weight:    0.6980
   chunk 77 optimal weight:    1.9990
   chunk 87 optimal weight:    2.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 393 GLN
C  69 GLN
C 232 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.089775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2818 r_free = 0.2818 target = 0.068149 restraints weight = 13136.039|
|-----------------------------------------------------------------------------|
r_work (start): 0.2805 rms_B_bonded: 2.78
r_work: 0.2688 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2561 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.1079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8082  Z= 0.174
  Angle     :  0.501   5.609  10983  Z= 0.269
  Chirality :  0.046   0.146   1174
  Planarity :  0.004   0.045   1446
  Dihedral  :  4.238  48.626   1114
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 23.95 %
    Favored  : 72.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.34 (0.27), residues: 975
  helix:  1.60 (0.58), residues: 91
  sheet:  0.21 (0.23), residues: 511
  loop : -1.26 (0.30), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 163 
 TYR   0.011   0.001   TYR A 537 
 PHE   0.008   0.001   PHE A 417 
 TRP   0.010   0.001   TRP A 465 
 HIS   0.004   0.001   HIS A 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 8082)
  covalent geometry    : angle       0.50101 (10983)
  hydrogen bonds       : bond        0.03722 (  306)
  hydrogen bonds       : angle       5.54275 (  861)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 77
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A  587 GLU cc_start: 0.7814 (mp0) cc_final: 0.7509 (tt0)
REVERT: A  674 THR cc_start: 0.8866 (OUTLIER) cc_final: 0.8500 (p)
REVERT: B  121 LYS cc_start: 0.8652 (ttmt) cc_final: 0.8432 (ttmt)
  outliers start: 30
  outliers final: 10
  residues processed: 96
  average time/residue: 0.4715
  time to fit residues: 48.4781
Evaluate side-chains
  83 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  452 LYS
Chi-restraints excluded: chain A residue  497 MET
Chi-restraints excluded: chain A residue  535 SER
Chi-restraints excluded: chain A residue  611 ASP
Chi-restraints excluded: chain A residue  674 THR
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  181 SER
Chi-restraints excluded: chain C residue  198 SER
Chi-restraints excluded: chain C residue  241 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 61 optimal weight:    4.9990
   chunk 60 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 39 optimal weight:    5.9990
   chunk 79 optimal weight:    5.9990
   chunk 12 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 85 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
C  69 GLN
C 232 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.089252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.067484 restraints weight = 13391.099|
|-----------------------------------------------------------------------------|
r_work (start): 0.2793 rms_B_bonded: 2.76
r_work: 0.2676 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2550 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.1184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   8082  Z= 0.212
  Angle     :  0.520   6.462  10983  Z= 0.279
  Chirality :  0.047   0.150   1174
  Planarity :  0.004   0.047   1446
  Dihedral  :  4.102  15.944   1113
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 23.95 %
    Favored  : 72.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.36 (0.27), residues: 975
  helix:  1.78 (0.61), residues: 86
  sheet:  0.24 (0.24), residues: 504
  loop : -1.32 (0.29), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 163 
 TYR   0.017   0.001   TYR A 278 
 PHE   0.010   0.001   PHE A 485 
 TRP   0.010   0.001   TRP A 465 
 HIS   0.004   0.001   HIS A 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00500 ( 8082)
  covalent geometry    : angle       0.51961 (10983)
  hydrogen bonds       : bond        0.03720 (  306)
  hydrogen bonds       : angle       5.48150 (  861)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 72
  time to evaluate  : 0.350 
Fit side-chains
REVERT: A  587 GLU cc_start: 0.7869 (mp0) cc_final: 0.7577 (tt0)
REVERT: A  674 THR cc_start: 0.8905 (OUTLIER) cc_final: 0.8545 (p)
REVERT: B  121 LYS cc_start: 0.8716 (ttmt) cc_final: 0.8463 (ttmt)
REVERT: C   23 ARG cc_start: 0.7543 (mpp80) cc_final: 0.6630 (mmm160)
  outliers start: 30
  outliers final: 14
  residues processed: 93
  average time/residue: 0.5535
  time to fit residues: 54.8730
Evaluate side-chains
  85 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 70
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 SER
Chi-restraints excluded: chain A residue  452 LYS
Chi-restraints excluded: chain A residue  497 MET
Chi-restraints excluded: chain A residue  535 SER
Chi-restraints excluded: chain A residue  611 ASP
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  674 THR
Chi-restraints excluded: chain A residue  783 THR
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   81 SER
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  198 SER
Chi-restraints excluded: chain C residue  241 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 65 optimal weight:    0.7980
   chunk 12 optimal weight:    3.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
C 232 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.089651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.067950 restraints weight = 13388.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.2804 rms_B_bonded: 2.76
r_work: 0.2690 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2563 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.1245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8082  Z= 0.181
  Angle     :  0.504   6.523  10983  Z= 0.270
  Chirality :  0.046   0.148   1174
  Planarity :  0.004   0.046   1446
  Dihedral  :  4.050  15.790   1113
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 23.25 %
    Favored  : 72.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.36 (0.27), residues: 975
  helix:  1.81 (0.61), residues: 86
  sheet:  0.25 (0.24), residues: 502
  loop : -1.33 (0.29), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 623 
 TYR   0.011   0.001   TYR A 244 
 PHE   0.007   0.001   PHE A 241 
 TRP   0.009   0.001   TRP A 465 
 HIS   0.004   0.001   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 8082)
  covalent geometry    : angle       0.50370 (10983)
  hydrogen bonds       : bond        0.03478 (  306)
  hydrogen bonds       : angle       5.35727 (  861)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 72
  time to evaluate  : 0.333 
Fit side-chains
REVERT: A  587 GLU cc_start: 0.7864 (mp0) cc_final: 0.7567 (tt0)
REVERT: A  648 GLU cc_start: 0.8447 (pt0) cc_final: 0.8193 (pt0)
REVERT: A  674 THR cc_start: 0.8878 (OUTLIER) cc_final: 0.8511 (p)
REVERT: A  772 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8134 (mtp)
REVERT: B  121 LYS cc_start: 0.8694 (ttmt) cc_final: 0.8428 (ttmt)
REVERT: C   23 ARG cc_start: 0.7617 (mpp80) cc_final: 0.6679 (mmm160)
  outliers start: 35
  outliers final: 18
  residues processed: 98
  average time/residue: 0.5308
  time to fit residues: 55.5662
Evaluate side-chains
  90 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 70
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 SER
Chi-restraints excluded: chain A residue  401 ASN
Chi-restraints excluded: chain A residue  452 LYS
Chi-restraints excluded: chain A residue  471 THR
Chi-restraints excluded: chain A residue  497 MET
Chi-restraints excluded: chain A residue  535 SER
Chi-restraints excluded: chain A residue  640 SER
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  674 THR
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue  783 THR
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   81 SER
Chi-restraints excluded: chain B residue  107 THR
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  181 SER
Chi-restraints excluded: chain C residue  198 SER
Chi-restraints excluded: chain C residue  241 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 86 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 24 optimal weight:    0.4980
   chunk 18 optimal weight:    0.6980
   chunk 82 optimal weight:    5.9990
   chunk 78 optimal weight:    0.3980
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 576 ASN
C 232 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.091420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.069760 restraints weight = 13215.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.2835 rms_B_bonded: 2.75
r_work: 0.2722 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2597 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.1344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8082  Z= 0.121
  Angle     :  0.473   6.247  10983  Z= 0.253
  Chirality :  0.045   0.142   1174
  Planarity :  0.004   0.045   1446
  Dihedral  :  3.877  14.508   1113
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 24.07 %
    Favored  : 72.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.27 (0.27), residues: 975
  helix:  1.77 (0.59), residues: 91
  sheet:  0.31 (0.24), residues: 491
  loop : -1.25 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 225 
 TYR   0.018   0.001   TYR A 278 
 PHE   0.011   0.001   PHE A 485 
 TRP   0.008   0.001   TRP A 465 
 HIS   0.003   0.001   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 8082)
  covalent geometry    : angle       0.47307 (10983)
  hydrogen bonds       : bond        0.03035 (  306)
  hydrogen bonds       : angle       5.12589 (  861)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 78
  time to evaluate  : 0.321 
Fit side-chains
REVERT: A  409 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7585 (ttp-110)
REVERT: A  469 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7394 (mtm110)
REVERT: A  587 GLU cc_start: 0.7843 (mp0) cc_final: 0.7520 (tt0)
REVERT: A  648 GLU cc_start: 0.8394 (pt0) cc_final: 0.8127 (pt0)
REVERT: A  674 THR cc_start: 0.8864 (OUTLIER) cc_final: 0.8488 (p)
REVERT: A  772 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.7998 (mtp)
REVERT: B  121 LYS cc_start: 0.8663 (ttmt) cc_final: 0.8389 (ttmt)
REVERT: C   23 ARG cc_start: 0.7629 (mpp80) cc_final: 0.7258 (mpp80)
  outliers start: 33
  outliers final: 17
  residues processed: 100
  average time/residue: 0.5387
  time to fit residues: 57.5575
Evaluate side-chains
  93 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 72
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  338 SER
Chi-restraints excluded: chain A residue  401 ASN
Chi-restraints excluded: chain A residue  409 ARG
Chi-restraints excluded: chain A residue  452 LYS
Chi-restraints excluded: chain A residue  469 ARG
Chi-restraints excluded: chain A residue  471 THR
Chi-restraints excluded: chain A residue  535 SER
Chi-restraints excluded: chain A residue  640 SER
Chi-restraints excluded: chain A residue  674 THR
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain B residue   81 SER
Chi-restraints excluded: chain B residue  107 THR
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  181 SER
Chi-restraints excluded: chain C residue  241 ILE
Chi-restraints excluded: chain C residue  263 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 24 optimal weight:    0.2980
   chunk 40 optimal weight:    0.5980
   chunk 81 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
C 232 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.091065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.069495 restraints weight = 13174.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.2812 rms_B_bonded: 2.73
r_work: 0.2694 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2568 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.1359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8082  Z= 0.132
  Angle     :  0.475   6.391  10983  Z= 0.254
  Chirality :  0.045   0.144   1174
  Planarity :  0.004   0.045   1446
  Dihedral  :  3.883  14.716   1113
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 24.65 %
    Favored  : 71.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.23 (0.27), residues: 975
  helix:  1.73 (0.59), residues: 92
  sheet:  0.33 (0.24), residues: 494
  loop : -1.21 (0.29), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 623 
 TYR   0.009   0.001   TYR C  27 
 PHE   0.006   0.001   PHE C 206 
 TRP   0.007   0.001   TRP A 465 
 HIS   0.003   0.001   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 8082)
  covalent geometry    : angle       0.47514 (10983)
  hydrogen bonds       : bond        0.03068 (  306)
  hydrogen bonds       : angle       5.08497 (  861)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 75
  time to evaluate  : 0.338 
Fit side-chains
REVERT: A  409 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7607 (ttp-110)
REVERT: A  469 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7383 (mtm110)
REVERT: A  587 GLU cc_start: 0.7884 (mp0) cc_final: 0.7570 (tt0)
REVERT: A  648 GLU cc_start: 0.8449 (pt0) cc_final: 0.8173 (pt0)
REVERT: A  674 THR cc_start: 0.8926 (OUTLIER) cc_final: 0.8560 (p)
REVERT: A  772 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8030 (mtp)
REVERT: B   99 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8570 (tp-100)
REVERT: B  121 LYS cc_start: 0.8719 (ttmt) cc_final: 0.8434 (ttmt)
REVERT: C   23 ARG cc_start: 0.7659 (mpp80) cc_final: 0.7317 (mpp80)
  outliers start: 30
  outliers final: 16
  residues processed: 98
  average time/residue: 0.5854
  time to fit residues: 61.0104
Evaluate side-chains
  93 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 72
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  338 SER
Chi-restraints excluded: chain A residue  401 ASN
Chi-restraints excluded: chain A residue  409 ARG
Chi-restraints excluded: chain A residue  452 LYS
Chi-restraints excluded: chain A residue  469 ARG
Chi-restraints excluded: chain A residue  471 THR
Chi-restraints excluded: chain A residue  497 MET
Chi-restraints excluded: chain A residue  535 SER
Chi-restraints excluded: chain A residue  640 SER
Chi-restraints excluded: chain A residue  674 THR
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain B residue   81 SER
Chi-restraints excluded: chain B residue   99 GLN
Chi-restraints excluded: chain B residue  107 THR
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  181 SER
Chi-restraints excluded: chain C residue  241 ILE
Chi-restraints excluded: chain C residue  263 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 56 optimal weight:    0.4980
   chunk 58 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 78 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   chunk 97 optimal weight:    0.8980
   chunk 91 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 92 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
C 232 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.091086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.069458 restraints weight = 13375.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.2812 rms_B_bonded: 2.75
r_work: 0.2693 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2566 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.1397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8082  Z= 0.135
  Angle     :  0.500  11.974  10983  Z= 0.263
  Chirality :  0.045   0.143   1174
  Planarity :  0.004   0.044   1446
  Dihedral  :  3.879  14.676   1113
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 24.42 %
    Favored  : 71.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.27), residues: 975
  helix:  1.80 (0.59), residues: 91
  sheet:  0.32 (0.24), residues: 494
  loop : -1.23 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 623 
 TYR   0.017   0.001   TYR A 278 
 PHE   0.014   0.001   PHE A 485 
 TRP   0.007   0.001   TRP A 465 
 HIS   0.006   0.001   HIS A 745 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 8082)
  covalent geometry    : angle       0.50037 (10983)
  hydrogen bonds       : bond        0.03050 (  306)
  hydrogen bonds       : angle       5.06105 (  861)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 78
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A  210 ILE cc_start: 0.7201 (OUTLIER) cc_final: 0.7000 (mt)
REVERT: A  409 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7647 (ttp-110)
REVERT: A  469 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7392 (mtm110)
REVERT: A  587 GLU cc_start: 0.7901 (mp0) cc_final: 0.7598 (tt0)
REVERT: A  648 GLU cc_start: 0.8471 (pt0) cc_final: 0.8185 (pt0)
REVERT: A  674 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8595 (p)
REVERT: B   99 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8613 (tp-100)
REVERT: B  121 LYS cc_start: 0.8753 (ttmt) cc_final: 0.8457 (ttmt)
REVERT: C   23 ARG cc_start: 0.7697 (mpp80) cc_final: 0.7367 (mpp80)
  outliers start: 31
  outliers final: 19
  residues processed: 103
  average time/residue: 0.5751
  time to fit residues: 62.9585
Evaluate side-chains
  96 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 72
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  338 SER
Chi-restraints excluded: chain A residue  401 ASN
Chi-restraints excluded: chain A residue  409 ARG
Chi-restraints excluded: chain A residue  452 LYS
Chi-restraints excluded: chain A residue  469 ARG
Chi-restraints excluded: chain A residue  471 THR
Chi-restraints excluded: chain A residue  497 MET
Chi-restraints excluded: chain A residue  535 SER
Chi-restraints excluded: chain A residue  640 SER
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  674 THR
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   81 SER
Chi-restraints excluded: chain B residue   99 GLN
Chi-restraints excluded: chain B residue  107 THR
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  181 SER
Chi-restraints excluded: chain C residue  241 ILE
Chi-restraints excluded: chain C residue  263 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 2 optimal weight:   10.0000
   chunk 47 optimal weight:    2.9990
   chunk 73 optimal weight:    0.6980
   chunk 77 optimal weight:    1.9990
   chunk 78 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
C  33 GLN
C 232 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.093666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.072443 restraints weight = 13224.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.2830 rms_B_bonded: 2.65
r_work: 0.2708 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2582 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.1428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8082  Z= 0.142
  Angle     :  0.504  11.659  10983  Z= 0.265
  Chirality :  0.045   0.144   1174
  Planarity :  0.004   0.044   1446
  Dihedral  :  3.913  14.798   1113
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 24.53 %
    Favored  : 72.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.27 (0.27), residues: 975
  helix:  1.81 (0.58), residues: 91
  sheet:  0.30 (0.24), residues: 494
  loop : -1.25 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 623 
 TYR   0.010   0.001   TYR C  27 
 PHE   0.006   0.001   PHE A 241 
 TRP   0.008   0.001   TRP A 465 
 HIS   0.004   0.001   HIS A 745 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 8082)
  covalent geometry    : angle       0.50406 (10983)
  hydrogen bonds       : bond        0.03088 (  306)
  hydrogen bonds       : angle       5.08055 (  861)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 77
  time to evaluate  : 0.337 
Fit side-chains
REVERT: A  210 ILE cc_start: 0.7228 (OUTLIER) cc_final: 0.7021 (mt)
REVERT: A  469 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7457 (mtm110)
REVERT: A  587 GLU cc_start: 0.7933 (mp0) cc_final: 0.7646 (tt0)
REVERT: A  648 GLU cc_start: 0.8498 (pt0) cc_final: 0.8210 (pt0)
REVERT: A  674 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8628 (p)
REVERT: B   99 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8659 (tp-100)
REVERT: B  100 MET cc_start: 0.8730 (ttt) cc_final: 0.8471 (mtp)
REVERT: B  121 LYS cc_start: 0.8800 (ttmt) cc_final: 0.8498 (ttmt)
REVERT: C   23 ARG cc_start: 0.7743 (mpp80) cc_final: 0.7421 (mpp80)
  outliers start: 29
  outliers final: 19
  residues processed: 100
  average time/residue: 0.5464
  time to fit residues: 58.1964
Evaluate side-chains
  98 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 75
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  338 SER
Chi-restraints excluded: chain A residue  401 ASN
Chi-restraints excluded: chain A residue  452 LYS
Chi-restraints excluded: chain A residue  469 ARG
Chi-restraints excluded: chain A residue  471 THR
Chi-restraints excluded: chain A residue  497 MET
Chi-restraints excluded: chain A residue  535 SER
Chi-restraints excluded: chain A residue  640 SER
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  674 THR
Chi-restraints excluded: chain A residue  783 THR
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   81 SER
Chi-restraints excluded: chain B residue   99 GLN
Chi-restraints excluded: chain B residue  107 THR
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  181 SER
Chi-restraints excluded: chain C residue  241 ILE
Chi-restraints excluded: chain C residue  263 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 96 optimal weight:    0.0060
   chunk 77 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 85 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 50 optimal weight:    0.0980
   chunk 83 optimal weight:    0.6980
   chunk 18 optimal weight:    0.7980
   chunk 26 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   overall best weight:    0.4796

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

Flipped N/Q/H residues before XYZ refinement:
A 744 GLN
B 131 GLN
C  33 GLN
C  69 GLN
C 232 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.095677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.074512 restraints weight = 13154.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.2860 rms_B_bonded: 2.67
r_work: 0.2736 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2610 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.1561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8082  Z= 0.103
  Angle     :  0.490  11.554  10983  Z= 0.255
  Chirality :  0.045   0.137   1174
  Planarity :  0.004   0.044   1446
  Dihedral  :  3.777  13.582   1113
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 25.58 %
    Favored  : 71.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.27), residues: 975
  helix:  1.88 (0.58), residues: 91
  sheet:  0.41 (0.24), residues: 483
  loop : -1.25 (0.29), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 623 
 TYR   0.016   0.001   TYR A 278 
 PHE   0.015   0.001   PHE A 485 
 TRP   0.007   0.001   TRP A 465 
 HIS   0.004   0.001   HIS A 745 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 8082)
  covalent geometry    : angle       0.48960 (10983)
  hydrogen bonds       : bond        0.02762 (  306)
  hydrogen bonds       : angle       4.89214 (  861)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 83
  time to evaluate  : 0.324 
Fit side-chains
REVERT: A  210 ILE cc_start: 0.7179 (OUTLIER) cc_final: 0.6966 (mt)
REVERT: A  409 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7704 (ttp-110)
REVERT: A  469 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7376 (mtm110)
REVERT: A  499 MET cc_start: 0.8845 (ppp) cc_final: 0.8585 (pmm)
REVERT: A  587 GLU cc_start: 0.7920 (mp0) cc_final: 0.7622 (tt0)
REVERT: A  648 GLU cc_start: 0.8449 (pt0) cc_final: 0.8178 (pt0)
REVERT: A  674 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8603 (p)
REVERT: B   99 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8602 (tp-100)
REVERT: B  121 LYS cc_start: 0.8770 (ttmt) cc_final: 0.8492 (ttmt)
REVERT: C   23 ARG cc_start: 0.7724 (mpp80) cc_final: 0.7411 (mpp80)
  outliers start: 22
  outliers final: 11
  residues processed: 102
  average time/residue: 0.4901
  time to fit residues: 53.2400
Evaluate side-chains
  93 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  401 ASN
Chi-restraints excluded: chain A residue  409 ARG
Chi-restraints excluded: chain A residue  469 ARG
Chi-restraints excluded: chain A residue  535 SER
Chi-restraints excluded: chain A residue  674 THR
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   81 SER
Chi-restraints excluded: chain B residue   99 GLN
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  181 SER
Chi-restraints excluded: chain C residue  241 ILE
Chi-restraints excluded: chain C residue  263 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 20 optimal weight:    0.3980
   chunk 73 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 27 optimal weight:    3.9990
   chunk 97 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 96 optimal weight:    0.6980
   chunk 36 optimal weight:    0.3980
   chunk 3 optimal weight:    0.8980
   chunk 90 optimal weight:    0.2980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
C  33 GLN
C  69 GLN
C 232 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.093906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.072394 restraints weight = 13190.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.2858 rms_B_bonded: 2.68
r_work: 0.2737 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2611 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.1594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8082  Z= 0.105
  Angle     :  0.494  10.910  10983  Z= 0.258
  Chirality :  0.045   0.140   1174
  Planarity :  0.004   0.043   1446
  Dihedral  :  3.770  13.406   1113
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 26.17 %
    Favored  : 71.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.13 (0.27), residues: 975
  helix:  1.91 (0.59), residues: 91
  sheet:  0.44 (0.24), residues: 482
  loop : -1.21 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 623 
 TYR   0.008   0.001   TYR C  27 
 PHE   0.006   0.001   PHE A 406 
 TRP   0.005   0.001   TRP C 168 
 HIS   0.003   0.001   HIS A 745 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 8082)
  covalent geometry    : angle       0.49408 (10983)
  hydrogen bonds       : bond        0.02800 (  306)
  hydrogen bonds       : angle       4.86342 (  861)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2892.46 seconds
wall clock time: 50 minutes 5.97 seconds (3005.97 seconds total)