Starting phenix.real_space_refine
on Tue Feb  3 22:44:21 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rpr_54169/02_2026/9rpr_54169.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rpr_54169/02_2026/9rpr_54169.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.78
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rpr_54169/02_2026/9rpr_54169.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rpr_54169/02_2026/9rpr_54169.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rpr_54169/02_2026/9rpr_54169.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rpr_54169/02_2026/9rpr_54169.map"
  }
  resolution = 2.78
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.011
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      29      5.16       5
     C    4662      2.51       5
     N    1272      2.21       5
     O    1440      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  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: 7403
  Number of models: 1
  Model: ""
    Number of chains: 4
    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: "A"
      Number of atoms: 5897
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 726, 5897
          Classifications: {'peptide': 726}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 697}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 264
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 264
          Classifications: {'peptide': 35}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 29}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 55
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 55
          Unusual residues: {'PLM': 1, 'PXS': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'PLM:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 1.32, per 1000 atoms: 0.18
  Number of scatterers: 7403
  At special positions: 0
  Unit cell: (102.12, 71.78, 107.3, 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      29     16.00
     O    1440      8.00
     N    1272      7.00
     C    4662      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  31 " - pdb=" SG  CYS A 724 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 173 " - pdb=" SG  CYS A 725 " distance=2.04

  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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.71
  Conformation dependent library (CDL) restraints added in 223.7 milliseconds
  

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1702

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 7 sheets defined
      11.7% alpha, 49.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'B' and resid 31 through 33
      No H-bonds generated for 'chain 'B' and resid 31 through 33'
    Processing helix  chain 'B' and resid 45 through 58
    Processing helix  chain 'B' and resid 129 through 131
      No H-bonds generated for 'chain 'B' and resid 129 through 131'
    Processing helix  chain 'B' and resid 132 through 157
    Processing helix  chain 'B' and resid 158 through 169
    Processing helix  chain 'A' and resid 26 through 31
    Processing helix  chain 'A' and resid 295 through 302
      removed outlier: 3.578A  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 463 through 469
      removed outlier: 4.080A  pdb=" N   ARG A 469 " --> pdb=" O   TRP A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 537 through 542
      removed outlier: 3.986A  pdb=" N   PHE A 541 " --> pdb=" O   SER A 538 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ARG A 542 " --> pdb=" O   GLY A 539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 668
    Processing helix  chain 'A' and resid 768 through 774
    Processing sheet with id=AA1, first strand: chain 'B' and resid 22 through 23
      removed outlier: 3.569A  pdb=" N   VAL A 478 " --> pdb=" O   TYR A 458 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   THR A 449 " --> pdb=" O   LEU A 438 " (cutoff:3.500A)
      removed outlier: 6.002A  pdb=" N   PHE A 406 " --> pdb=" O   ASP A 402 " (cutoff:3.500A)
      removed outlier: 7.150A  pdb=" N   VAL A 418 " --> pdb=" O   ALA A 390 " (cutoff:3.500A)
      removed outlier: 5.619A  pdb=" N   ALA A 390 " --> pdb=" O   VAL A 418 " (cutoff:3.500A)
      removed outlier: 7.393A  pdb=" N   SER A 389 " --> pdb=" O   PHE A 377 " (cutoff:3.500A)
      removed outlier: 8.320A  pdb=" N   PHE A 377 " --> pdb=" O   SER A 389 " (cutoff:3.500A)
      removed outlier: 5.411A  pdb=" N   GLU A 391 " --> pdb=" O   LYS A 375 " (cutoff:3.500A)
      removed outlier: 7.936A  pdb=" N   LYS A 375 " --> pdb=" O   GLU A 391 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   PHE A 368 " --> pdb=" O   VAL A 365 " (cutoff:3.500A)
      removed outlier: 11.128A  pdb=" N   TYR A 354 " --> pdb=" O   VAL A 334 " (cutoff:3.500A)
      removed outlier: 8.861A  pdb=" N   VAL A 334 " --> pdb=" O   TYR A 354 " (cutoff:3.500A)
      removed outlier: 4.634A  pdb=" N   THR A 356 " --> pdb=" O   THR A 332 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   TYR A 278 " --> pdb=" O   GLY A 285 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   ASN A 269 " --> pdb=" O   MET A 264 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   MET A 264 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   MET A 255 " --> pdb=" O   ILE A 251 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ILE A 251 " --> pdb=" O   MET A 255 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 22 through 23
      removed outlier: 7.648A  pdb=" N   ASN A 556 " --> pdb=" O   TYR A 584 " (cutoff:3.500A)
      removed outlier: 4.908A  pdb=" N   TYR A 584 " --> pdb=" O   ASN A 556 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   VAL A 558 " --> pdb=" O   ILE A 582 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   ILE A 582 " --> pdb=" O   VAL A 558 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   THR A 560 " --> pdb=" O   GLY A 580 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   GLY A 580 " --> pdb=" O   THR A 560 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   VAL A 562 " --> pdb=" O   SER A 578 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   SER A 578 " --> pdb=" O   VAL A 562 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   SER A 564 " --> pdb=" O   ASN A 576 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   ASN A 576 " --> pdb=" O   SER A 564 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   ILE A 566 " --> pdb=" O   ARG A 574 " (cutoff:3.500A)
      removed outlier: 8.349A  pdb=" N   ARG A 574 " --> pdb=" O   TRP A 614 " (cutoff:3.500A)
      removed outlier: 4.645A  pdb=" N   TRP A 614 " --> pdb=" O   ARG A 574 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   ASN A 576 " --> pdb=" O   THR A 612 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   THR A 612 " --> pdb=" O   ASN A 576 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   SER A 578 " --> pdb=" O   GLY A 610 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   GLY A 610 " --> pdb=" O   SER A 578 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   GLY A 580 " --> pdb=" O   TRP A 608 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   TRP A 608 " --> pdb=" O   GLY A 580 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   ILE A 582 " --> pdb=" O   LEU A 606 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   THR A 637 " --> pdb=" O   GLN A 627 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   ASP A 629 " --> pdb=" O   VAL A 635 " (cutoff:3.500A)
      removed outlier: 5.494A  pdb=" N   VAL A 635 " --> pdb=" O   ASP A 629 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   ARG A 650 " --> pdb=" O   ARG A 646 " (cutoff:3.500A)
      removed outlier: 5.444A  pdb=" N   ASP A 706 " --> pdb=" O   GLN A 712 " (cutoff:3.500A)
      removed outlier: 5.481A  pdb=" N   GLN A 712 " --> pdb=" O   ASP A 706 " (cutoff:3.500A)
      removed outlier: 13.217A  pdb=" N   LYS A 711 " --> pdb=" O   GLY A 738 " (cutoff:3.500A)
      removed outlier: 13.188A  pdb=" N   GLY A 738 " --> pdb=" O   LYS A 711 " (cutoff:3.500A)
      removed outlier: 8.712A  pdb=" N   ALA A 713 " --> pdb=" O   LEU A 736 " (cutoff:3.500A)
      removed outlier: 5.557A  pdb=" N   VAL A 747 " --> pdb=" O   ASN A 737 " (cutoff:3.500A)
      removed outlier: 5.233A  pdb=" N   TRP A 739 " --> pdb=" O   HIS A 745 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   HIS A 745 " --> pdb=" O   TRP A 739 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ALA A 233 " --> pdb=" O   PHE A 754 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   MET A 255 " --> pdb=" O   ILE A 251 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ILE A 251 " --> pdb=" O   MET A 255 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 63
      removed outlier: 6.925A  pdb=" N   MET B  36 " --> pdb=" O   LEU B  63 " (cutoff:3.500A)
      removed outlier: 7.992A  pdb=" N   LEU B  75 " --> pdb=" O   VAL B  35 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   ILE B  37 " --> pdb=" O   LEU B  75 " (cutoff:3.500A)
      removed outlier: 7.450A  pdb=" N   LEU B  77 " --> pdb=" O   ILE B  37 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   ASP B  39 " --> pdb=" O   LEU B  77 " (cutoff:3.500A)
      removed outlier: 9.201A  pdb=" N   LYS B  79 " --> pdb=" O   ASP B  39 " (cutoff:3.500A)
      removed outlier: 5.707A  pdb=" N   LEU B  75 " --> pdb=" O   LEU B 109 " (cutoff:3.500A)
      removed outlier: 7.120A  pdb=" N   LEU B 109 " --> pdb=" O   LEU B  75 " (cutoff:3.500A)
      removed outlier: 5.393A  pdb=" N   LEU B  77 " --> pdb=" O   THR B 107 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   THR B 107 " --> pdb=" O   LEU B  77 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   LYS B  79 " --> pdb=" O   ASN B 105 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   GLU B  97 " --> pdb=" O   ALA B  87 " (cutoff:3.500A)
      removed outlier: 6.248A  pdb=" N   VAL B  89 " --> pdb=" O   THR B  95 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   THR B  95 " --> pdb=" O   VAL B  89 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 61 through 63
      removed outlier: 6.925A  pdb=" N   MET B  36 " --> pdb=" O   LEU B  63 " (cutoff:3.500A)
      removed outlier: 7.992A  pdb=" N   LEU B  75 " --> pdb=" O   VAL B  35 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   ILE B  37 " --> pdb=" O   LEU B  75 " (cutoff:3.500A)
      removed outlier: 7.450A  pdb=" N   LEU B  77 " --> pdb=" O   ILE B  37 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   ASP B  39 " --> pdb=" O   LEU B  77 " (cutoff:3.500A)
      removed outlier: 9.201A  pdb=" N   LYS B  79 " --> pdb=" O   ASP B  39 " (cutoff:3.500A)
      removed outlier: 9.031A  pdb=" N   ASP C  52 " --> pdb=" O   VAL B  80 " (cutoff:3.500A)
      removed outlier: 7.301A  pdb=" N   ILE B  82 " --> pdb=" O   ASP C  52 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 75 through 77
      removed outlier: 3.742A  pdb=" N   ILE A  75 " --> pdb=" O   LEU A  82 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   SER A  80 " --> pdb=" O   GLN A  77 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 86 through 90
      removed outlier: 3.521A  pdb=" N   ALA A 106 " --> pdb=" O   GLY A 124 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   VAL A 110 " --> pdb=" O   LYS A 120 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   LYS A 120 " --> pdb=" O   VAL A 110 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   GLY A 121 " --> pdb=" O   GLY A 138 " (cutoff:3.500A)
      removed outlier: 7.130A  pdb=" N   GLY A 138 " --> pdb=" O   GLY A 121 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   LYS A 123 " --> pdb=" O   TRP A 136 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ASP A 132 " --> pdb=" O   ASN A 127 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   GLN A 156 " --> pdb=" O   THR A 133 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   ASP A 152 " --> pdb=" O   GLU A 137 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   LEU A 153 " --> pdb=" O   ASP A 166 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 180 through 183
      removed outlier: 7.076A  pdb=" N   ALA A 201 " --> pdb=" O   TYR A 212 " (cutoff:3.500A)
      removed outlier: 4.656A  pdb=" N   TYR A 212 " --> pdb=" O   ALA A 201 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   PHE A 203 " --> pdb=" O   ILE A 210 " (cutoff:3.500A)

    358 hydrogen bonds defined for protein.
    993 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: 1.46

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1252
        1.31 -     1.44: 2168
        1.44 -     1.56: 4104
        1.56 -     1.69: 0
        1.69 -     1.82: 52
  Bond restraints: 7576
  Sorted by residual:
  bond pdb=" C1  PLM C 101 "
       pdb=" O2  PLM C 101 "
    ideal  model  delta    sigma   weight residual
    1.249  1.177  0.072 2.00e-02 2.50e+03 1.29e+01
  bond pdb=" C16 PXS C 102 "
       pdb=" O17 PXS C 102 "
    ideal  model  delta    sigma   weight residual
    1.330  1.402 -0.072 2.00e-02 2.50e+03 1.28e+01
  bond pdb=" C22 PXS C 102 "
       pdb=" O21 PXS C 102 "
    ideal  model  delta    sigma   weight residual
    1.331  1.394 -0.063 2.00e-02 2.50e+03 9.93e+00
  bond pdb=" C   CYS C  20A"
       pdb=" O   CYS C  20A"
    ideal  model  delta    sigma   weight residual
    1.231  1.178  0.053 2.00e-02 2.50e+03 7.14e+00
  bond pdb=" C19 PXS C 102 "
       pdb=" O21 PXS C 102 "
    ideal  model  delta    sigma   weight residual
    1.438  1.388  0.050 2.00e-02 2.50e+03 6.33e+00
  ... (remaining 7571 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 10128
        2.09 -     4.17: 134
        4.17 -     6.26: 10
        6.26 -     8.35: 0
        8.35 -    10.43: 2
  Bond angle restraints: 10274
  Sorted by residual:
  angle pdb=" C23 PXS C 102 "
        pdb=" C22 PXS C 102 "
        pdb=" O21 PXS C 102 "
      ideal   model   delta    sigma   weight residual
     111.52  121.95  -10.43 3.00e+00 1.11e-01 1.21e+01
  angle pdb=" C15 PXS C 102 "
        pdb=" C16 PXS C 102 "
        pdb=" O17 PXS C 102 "
      ideal   model   delta    sigma   weight residual
     111.74  120.63   -8.89 3.00e+00 1.11e-01 8.77e+00
  angle pdb=" CA  TYR A 215 "
        pdb=" CB  TYR A 215 "
        pdb=" CG  TYR A 215 "
      ideal   model   delta    sigma   weight residual
     113.90  109.17    4.73 1.80e+00 3.09e-01 6.92e+00
  angle pdb=" N   SER A 185 "
        pdb=" CA  SER A 185 "
        pdb=" C   SER A 185 "
      ideal   model   delta    sigma   weight residual
     114.64  110.86    3.78 1.52e+00 4.33e-01 6.20e+00
  angle pdb=" C   TYR A 240 "
        pdb=" CA  TYR A 240 "
        pdb=" CB  TYR A 240 "
      ideal   model   delta    sigma   weight residual
     110.42  115.35   -4.93 1.99e+00 2.53e-01 6.14e+00
  ... (remaining 10269 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.87: 4141
       17.87 -    35.75: 269
       35.75 -    53.62: 77
       53.62 -    71.49: 22
       71.49 -    89.36: 11
  Dihedral angle restraints: 4520
    sinusoidal: 1851
      harmonic: 2669
  Sorted by residual:
  dihedral pdb=" CA  TYR A 678 "
           pdb=" C   TYR A 678 "
           pdb=" N   LYS A 679 "
           pdb=" CA  LYS A 679 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.50  -20.50     0      5.00e+00 4.00e-02 1.68e+01
  dihedral pdb=" CA  ASN A 556 "
           pdb=" C   ASN A 556 "
           pdb=" N   GLN A 557 "
           pdb=" CA  GLN A 557 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.19  -17.81     0      5.00e+00 4.00e-02 1.27e+01
  dihedral pdb=" CA  LYS A 234 "
           pdb=" C   LYS A 234 "
           pdb=" N   TYR A 235 "
           pdb=" CA  TYR A 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.65   17.35     0      5.00e+00 4.00e-02 1.20e+01
  ... (remaining 4517 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 547
       0.030 -    0.060: 318
       0.060 -    0.090: 118
       0.090 -    0.120: 73
       0.120 -    0.150: 19
  Chirality restraints: 1075
  Sorted by residual:
  chirality pdb=" CA  ILE A 525 "
            pdb=" N   ILE A 525 "
            pdb=" C   ILE A 525 "
            pdb=" CB  ILE A 525 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.65e-01
  chirality pdb=" CA  ILE B  37 "
            pdb=" N   ILE B  37 "
            pdb=" C   ILE B  37 "
            pdb=" CB  ILE B  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.40e-01
  chirality pdb=" CA  ILE B 110 "
            pdb=" N   ILE B 110 "
            pdb=" C   ILE B 110 "
            pdb=" CB  ILE B 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.90e-01
  ... (remaining 1072 not shown)

  Planarity restraints: 1351
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 391 "    0.029 5.00e-02 4.00e+02   4.41e-02 3.11e+00
        pdb=" N   PRO A 392 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A 392 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 392 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 260 "    0.029 5.00e-02 4.00e+02   4.36e-02 3.04e+00
        pdb=" N   PRO A 261 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO A 261 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 261 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 482 "    0.027 5.00e-02 4.00e+02   4.15e-02 2.75e+00
        pdb=" N   PRO A 483 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO A 483 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 483 "    0.023 5.00e-02 4.00e+02
  ... (remaining 1348 not shown)

  Histogram of nonbonded interaction distances:
        1.30 -     2.02: 1
        2.02 -     2.74: 546
        2.74 -     3.46: 9360
        3.46 -     4.18: 17531
        4.18 -     4.90: 32754
  Nonbonded interactions: 60192
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A 225 "
            pdb=" O   CYS C  20A"
     model   vdw
     1.298 3.120
  nonbonded pdb=" CZ  ARG A 225 "
            pdb=" O   CYS C  20A"
     model   vdw
     2.376 3.270
  nonbonded pdb=" NH2 ARG A 225 "
            pdb=" C   CYS C  20A"
     model   vdw
     2.396 3.350
  nonbonded pdb=" CB  ARG A 409 "
            pdb=" NE  ARG A 409 "
     model   vdw
     2.522 2.816
  nonbonded pdb=" OD1 ASP A 529 "
            pdb=" OD2 ASP A 550 "
     model   vdw
     2.583 3.040
  ... (remaining 60187 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:             3.710
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.760
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8749
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      :  0.007   0.072   7580  Z= 0.306
  Angle     :  0.636  10.432  10278  Z= 0.336
  Chirality :  0.049   0.150   1075
  Planarity :  0.006   0.044   1351
  Dihedral  : 14.278  89.363   2812
  Min Nonbonded Distance : 1.298

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  :  8.17 %
    Favored  : 89.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -0.76 (0.27), residues: 900
  helix: -0.39 (0.52), residues: 86
  sheet:  0.13 (0.25), residues: 432
  loop : -1.21 (0.28), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 225 
 TYR   0.022   0.002   TYR A 244 
 PHE   0.018   0.002   PHE A 211 
 TRP   0.010   0.001   TRP A 180 
 HIS   0.004   0.001   HIS A 431 

Details of bonding type rmsd
  covalent geometry    : bond        0.00700 ( 7576)
  covalent geometry    : angle       0.63526 (10274)
  SS BOND              : bond        0.00589 (    2)
  SS BOND              : angle       1.37054 (    4)
  hydrogen bonds       : bond        0.19678 (  346)
  hydrogen bonds       : angle       8.52785 (  993)
  Misc. bond           : bond        0.05056 (    2)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
REVERT: B  109 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8830 (tp)
REVERT: A  326 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.7592 (mtm180)
REVERT: A  699 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8756 (mm)
  outliers start: 17
  outliers final: 4
  residues processed: 107
  average time/residue: 0.6278
  time to fit residues: 70.4907
Evaluate side-chains
  77 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  326 ARG
Chi-restraints excluded: chain A residue  574 ARG
Chi-restraints excluded: chain A residue  699 ILE
Chi-restraints excluded: chain C residue   20 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0670
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.7720

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

Flipped N/Q/H residues before XYZ refinement:
A 599 ASN
** A 745 HIS ** 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 = 0.3285 r_free = 0.3285 target = 0.097592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.072712 restraints weight = 11169.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.2895 rms_B_bonded: 2.44
r_work: 0.2767 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2628 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.1265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   7580  Z= 0.126
  Angle     :  0.503   5.268  10278  Z= 0.279
  Chirality :  0.045   0.144   1075
  Planarity :  0.005   0.043   1351
  Dihedral  :  8.249  64.998   1090
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 12.56 %
    Favored  : 85.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -0.17 (0.27), residues: 900
  helix:  1.48 (0.56), residues: 87
  sheet:  0.45 (0.25), residues: 433
  loop : -1.13 (0.29), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 469 
 TYR   0.016   0.001   TYR C  67 
 PHE   0.013   0.001   PHE A 211 
 TRP   0.007   0.001   TRP A 180 
 HIS   0.002   0.001   HIS A 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 7576)
  covalent geometry    : angle       0.50311 (10274)
  SS BOND              : bond        0.00215 (    2)
  SS BOND              : angle       0.72211 (    4)
  hydrogen bonds       : bond        0.04251 (  346)
  hydrogen bonds       : angle       5.74591 (  993)
  Misc. bond           : bond        0.00055 (    2)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 0.244 
Fit side-chains
REVERT: B   53 ASN cc_start: 0.8537 (t0) cc_final: 0.8132 (m110)
REVERT: A  160 ASN cc_start: 0.7074 (p0) cc_final: 0.6324 (t0)
REVERT: A  167 ASN cc_start: 0.8202 (t0) cc_final: 0.7846 (t0)
REVERT: A  344 ASP cc_start: 0.8384 (t0) cc_final: 0.8142 (t0)
REVERT: A  648 GLU cc_start: 0.8716 (tt0) cc_final: 0.8092 (tp30)
REVERT: A  699 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8347 (mm)
  outliers start: 15
  outliers final: 3
  residues processed: 86
  average time/residue: 0.5536
  time to fit residues: 50.3091
Evaluate side-chains
  74 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 70
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  699 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 75 optimal weight:    0.5980
   chunk 60 optimal weight:    3.9990
   chunk 64 optimal weight:    0.5980
   chunk 78 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 28 optimal weight:    5.9990
   chunk 87 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 65 optimal weight:    0.5980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A  77 GLN
A 599 ASN
** A 745 HIS ** 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 = 0.3310 r_free = 0.3310 target = 0.099758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.076292 restraints weight = 11582.730|
|-----------------------------------------------------------------------------|
r_work (start): 0.2907 rms_B_bonded: 2.48
r_work: 0.2780 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2649 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8536
moved from start:          0.1595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7580  Z= 0.131
  Angle     :  0.493   9.448  10278  Z= 0.264
  Chirality :  0.045   0.143   1075
  Planarity :  0.005   0.044   1351
  Dihedral  :  7.378  63.146   1078
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 13.94 %
    Favored  : 84.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  0.04 (0.28), residues: 900
  helix:  2.00 (0.56), residues: 89
  sheet:  0.55 (0.25), residues: 434
  loop : -1.06 (0.30), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 469 
 TYR   0.016   0.001   TYR C  67 
 PHE   0.012   0.001   PHE A 211 
 TRP   0.007   0.001   TRP A 180 
 HIS   0.002   0.001   HIS A 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 7576)
  covalent geometry    : angle       0.49243 (10274)
  SS BOND              : bond        0.00219 (    2)
  SS BOND              : angle       0.67713 (    4)
  hydrogen bonds       : bond        0.03694 (  346)
  hydrogen bonds       : angle       5.25393 (  993)
  Misc. bond           : bond        0.00065 (    2)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.323 
Fit side-chains
REVERT: B   53 ASN cc_start: 0.8740 (t0) cc_final: 0.8446 (t0)
REVERT: A  102 ARG cc_start: 0.6561 (OUTLIER) cc_final: 0.5873 (mtm180)
REVERT: A  344 ASP cc_start: 0.8328 (t0) cc_final: 0.8079 (t0)
REVERT: A  648 GLU cc_start: 0.8747 (tt0) cc_final: 0.8064 (tp30)
  outliers start: 14
  outliers final: 4
  residues processed: 82
  average time/residue: 0.5159
  time to fit residues: 44.9215
Evaluate side-chains
  70 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  102 ARG
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  312 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 3 optimal weight:    0.5980
   chunk 38 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 69 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 81 optimal weight:    5.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
A  77 GLN
A 160 ASN
A 599 ASN
A 745 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.097377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.073251 restraints weight = 11938.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.2863 rms_B_bonded: 2.55
r_work: 0.2738 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2606 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.1502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053   7580  Z= 0.236
  Angle     :  0.553   8.326  10278  Z= 0.299
  Chirality :  0.047   0.161   1075
  Planarity :  0.005   0.049   1351
  Dihedral  :  7.486  63.868   1076
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 2.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 14.95 %
    Favored  : 82.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -0.06 (0.28), residues: 900
  helix:  2.01 (0.56), residues: 89
  sheet:  0.49 (0.25), residues: 436
  loop : -1.18 (0.29), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 469 
 TYR   0.017   0.002   TYR A 215 
 PHE   0.016   0.001   PHE A 211 
 TRP   0.009   0.001   TRP A 180 
 HIS   0.003   0.001   HIS A 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00570 ( 7576)
  covalent geometry    : angle       0.55298 (10274)
  SS BOND              : bond        0.00323 (    2)
  SS BOND              : angle       0.95358 (    4)
  hydrogen bonds       : bond        0.04332 (  346)
  hydrogen bonds       : angle       5.35432 (  993)
  Misc. bond           : bond        0.00102 (    2)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 68
  time to evaluate  : 0.264 
Fit side-chains
REVERT: B   53 ASN cc_start: 0.8673 (t0) cc_final: 0.8368 (t0)
REVERT: A  102 ARG cc_start: 0.6551 (OUTLIER) cc_final: 0.5884 (mtm180)
REVERT: A  344 ASP cc_start: 0.8378 (t0) cc_final: 0.8091 (t0)
REVERT: A  598 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7157 (mp0)
REVERT: A  648 GLU cc_start: 0.8764 (tt0) cc_final: 0.8126 (tp30)
  outliers start: 19
  outliers final: 7
  residues processed: 79
  average time/residue: 0.5109
  time to fit residues: 43.0121
Evaluate side-chains
  75 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain A residue  102 ARG
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  160 ASN
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  578 SER
Chi-restraints excluded: chain A residue  598 GLU
Chi-restraints excluded: chain A residue  745 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   chunk 76 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 19 optimal weight:    9.9990
   chunk 34 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A  77 GLN
A 160 ASN
A 599 ASN
** A 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.098515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.074386 restraints weight = 11799.503|
|-----------------------------------------------------------------------------|
r_work (start): 0.2881 rms_B_bonded: 2.55
r_work: 0.2755 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2624 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.1643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   7580  Z= 0.168
  Angle     :  0.520   8.315  10278  Z= 0.280
  Chirality :  0.046   0.144   1075
  Planarity :  0.005   0.048   1351
  Dihedral  :  7.356  62.327   1076
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 15.45 %
    Favored  : 82.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -0.02 (0.28), residues: 900
  helix:  2.16 (0.56), residues: 89
  sheet:  0.45 (0.25), residues: 443
  loop : -1.12 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 469 
 TYR   0.016   0.001   TYR C  67 
 PHE   0.014   0.001   PHE A 211 
 TRP   0.009   0.001   TRP A 180 
 HIS   0.005   0.001   HIS A 745 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 7576)
  covalent geometry    : angle       0.51991 (10274)
  SS BOND              : bond        0.00262 (    2)
  SS BOND              : angle       0.85907 (    4)
  hydrogen bonds       : bond        0.03847 (  346)
  hydrogen bonds       : angle       5.18488 (  993)
  Misc. bond           : bond        0.00074 (    2)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 68
  time to evaluate  : 0.353 
Fit side-chains
REVERT: B   53 ASN cc_start: 0.8690 (t0) cc_final: 0.8371 (t0)
REVERT: A   32 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8562 (ttm)
REVERT: A  102 ARG cc_start: 0.6605 (OUTLIER) cc_final: 0.5932 (mtm180)
REVERT: A  142 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.6333 (mpt)
REVERT: A  160 ASN cc_start: 0.6619 (OUTLIER) cc_final: 0.5474 (t0)
REVERT: A  344 ASP cc_start: 0.8361 (t0) cc_final: 0.8079 (t0)
REVERT: A  598 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7166 (mp0)
REVERT: A  648 GLU cc_start: 0.8760 (tt0) cc_final: 0.8119 (tp30)
  outliers start: 20
  outliers final: 8
  residues processed: 80
  average time/residue: 0.5143
  time to fit residues: 43.8703
Evaluate side-chains
  77 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  102 ARG
Chi-restraints excluded: chain A residue  142 MET
Chi-restraints excluded: chain A residue  160 ASN
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  578 SER
Chi-restraints excluded: chain A residue  598 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 39 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 83 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 89 optimal weight:    6.9990
   chunk 20 optimal weight:   10.0000
   chunk 44 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 85 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
A  77 GLN
A 160 ASN
A 345 ASN
A 599 ASN
** A 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.097965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.073910 restraints weight = 11843.265|
|-----------------------------------------------------------------------------|
r_work (start): 0.2877 rms_B_bonded: 2.54
r_work: 0.2753 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2621 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.1680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067   7580  Z= 0.195
  Angle     :  0.530   7.927  10278  Z= 0.286
  Chirality :  0.046   0.145   1075
  Planarity :  0.005   0.050   1351
  Dihedral  :  7.351  61.357   1076
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 16.58 %
    Favored  : 81.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -0.01 (0.28), residues: 900
  helix:  2.17 (0.56), residues: 89
  sheet:  0.52 (0.25), residues: 434
  loop : -1.18 (0.30), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 469 
 TYR   0.016   0.001   TYR C  67 
 PHE   0.014   0.001   PHE A 211 
 TRP   0.009   0.001   TRP A 180 
 HIS   0.003   0.001   HIS A 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00469 ( 7576)
  covalent geometry    : angle       0.52969 (10274)
  SS BOND              : bond        0.00286 (    2)
  SS BOND              : angle       0.93170 (    4)
  hydrogen bonds       : bond        0.03970 (  346)
  hydrogen bonds       : angle       5.18340 (  993)
  Misc. bond           : bond        0.00084 (    2)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
REVERT: B   53 ASN cc_start: 0.8661 (t0) cc_final: 0.8338 (t0)
REVERT: A  102 ARG cc_start: 0.6600 (OUTLIER) cc_final: 0.5949 (mtm180)
REVERT: A  142 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.6347 (mpt)
REVERT: A  160 ASN cc_start: 0.6730 (OUTLIER) cc_final: 0.5723 (t0)
REVERT: A  344 ASP cc_start: 0.8364 (t0) cc_final: 0.8066 (t0)
REVERT: A  598 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7168 (mp0)
REVERT: A  648 GLU cc_start: 0.8782 (tt0) cc_final: 0.8122 (tp30)
  outliers start: 16
  outliers final: 9
  residues processed: 82
  average time/residue: 0.4645
  time to fit residues: 40.5047
Evaluate side-chains
  78 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain A residue  102 ARG
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  142 MET
Chi-restraints excluded: chain A residue  160 ASN
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  578 SER
Chi-restraints excluded: chain A residue  598 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 18 optimal weight:    7.9990
   chunk 6 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 69 optimal weight:    4.9990
   chunk 22 optimal weight:    8.9990
   chunk 5 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9980
   chunk 20 optimal weight:    7.9990
   chunk 3 optimal weight:    0.0170
   chunk 82 optimal weight:    0.8980
   overall best weight:    0.7618

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

Flipped N/Q/H residues before XYZ refinement:
B  92 ASN
A 160 ASN
A 576 ASN
A 599 ASN
A 745 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.100023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.075985 restraints weight = 11815.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.2912 rms_B_bonded: 2.56
r_work: 0.2788 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2656 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.1890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   7580  Z= 0.119
  Angle     :  0.495   7.235  10278  Z= 0.265
  Chirality :  0.045   0.146   1075
  Planarity :  0.005   0.051   1351
  Dihedral  :  7.162  59.856   1076
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 2.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 17.84 %
    Favored  : 80.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  0.16 (0.28), residues: 900
  helix:  2.43 (0.56), residues: 89
  sheet:  0.63 (0.25), residues: 432
  loop : -1.10 (0.30), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A 469 
 TYR   0.015   0.001   TYR C  67 
 PHE   0.011   0.001   PHE A 211 
 TRP   0.008   0.001   TRP A 180 
 HIS   0.002   0.001   HIS A 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 7576)
  covalent geometry    : angle       0.49493 (10274)
  SS BOND              : bond        0.00212 (    2)
  SS BOND              : angle       0.73756 (    4)
  hydrogen bonds       : bond        0.03373 (  346)
  hydrogen bonds       : angle       4.97072 (  993)
  Misc. bond           : bond        0.00049 (    2)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
REVERT: B   19 CYS cc_start: 0.6720 (t) cc_final: 0.6460 (p)
REVERT: B   53 ASN cc_start: 0.8658 (t0) cc_final: 0.8331 (t0)
REVERT: A   32 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8502 (ttm)
REVERT: A  160 ASN cc_start: 0.6824 (OUTLIER) cc_final: 0.5943 (t0)
REVERT: A  344 ASP cc_start: 0.8335 (t0) cc_final: 0.8064 (t0)
REVERT: A  648 GLU cc_start: 0.8757 (tt0) cc_final: 0.8101 (tp30)
  outliers start: 12
  outliers final: 5
  residues processed: 75
  average time/residue: 0.4920
  time to fit residues: 39.3129
Evaluate side-chains
  72 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue  160 ASN
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  590 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 65 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   chunk 49 optimal weight:    0.3980
   chunk 84 optimal weight:    0.3980
   chunk 13 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 24 optimal weight:    8.9990
   chunk 54 optimal weight:    1.9990
   chunk 72 optimal weight:    4.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 160 ASN
A 599 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.099631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.075521 restraints weight = 11925.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.2907 rms_B_bonded: 2.57
r_work: 0.2783 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2650 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.1920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076   7580  Z= 0.132
  Angle     :  0.496   6.946  10278  Z= 0.266
  Chirality :  0.045   0.153   1075
  Planarity :  0.005   0.050   1351
  Dihedral  :  7.104  59.441   1076
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 2.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 17.34 %
    Favored  : 80.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  0.21 (0.28), residues: 900
  helix:  2.47 (0.55), residues: 89
  sheet:  0.67 (0.25), residues: 432
  loop : -1.06 (0.30), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 469 
 TYR   0.015   0.001   TYR C  67 
 PHE   0.011   0.001   PHE A 211 
 TRP   0.008   0.001   TRP A 180 
 HIS   0.003   0.001   HIS A 745 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 7576)
  covalent geometry    : angle       0.49563 (10274)
  SS BOND              : bond        0.00223 (    2)
  SS BOND              : angle       0.76063 (    4)
  hydrogen bonds       : bond        0.03434 (  346)
  hydrogen bonds       : angle       4.92745 (  993)
  Misc. bond           : bond        0.00053 (    2)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 73
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   19 CYS cc_start: 0.6791 (t) cc_final: 0.6561 (p)
REVERT: B   53 ASN cc_start: 0.8657 (t0) cc_final: 0.8326 (t0)
REVERT: A  159 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8282 (OUTLIER)
REVERT: A  160 ASN cc_start: 0.6897 (OUTLIER) cc_final: 0.6113 (OUTLIER)
REVERT: A  344 ASP cc_start: 0.8322 (t0) cc_final: 0.8053 (t0)
REVERT: A  648 GLU cc_start: 0.8755 (tt0) cc_final: 0.8126 (tp30)
  outliers start: 17
  outliers final: 11
  residues processed: 84
  average time/residue: 0.4761
  time to fit residues: 42.7086
Evaluate side-chains
  78 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain A residue   35 VAL
Chi-restraints excluded: chain A residue  160 ASN
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  578 SER
Chi-restraints excluded: chain A residue  590 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 80 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 79 optimal weight:    0.6980
   chunk 75 optimal weight:    0.0980
   chunk 42 optimal weight:    3.9990
   chunk 23 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 160 ASN
A 599 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.098839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.074794 restraints weight = 11730.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.2891 rms_B_bonded: 2.55
r_work: 0.2765 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2633 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8485
moved from start:          0.1895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.081   7580  Z= 0.170
  Angle     :  0.530   7.222  10278  Z= 0.282
  Chirality :  0.046   0.156   1075
  Planarity :  0.005   0.050   1351
  Dihedral  :  7.187  59.761   1076
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 2.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 17.84 %
    Favored  : 80.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  0.17 (0.28), residues: 900
  helix:  2.43 (0.55), residues: 89
  sheet:  0.59 (0.25), residues: 441
  loop : -1.05 (0.30), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 469 
 TYR   0.016   0.001   TYR C  67 
 PHE   0.013   0.001   PHE A 211 
 TRP   0.007   0.001   TRP A 180 
 HIS   0.003   0.001   HIS A 745 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 7576)
  covalent geometry    : angle       0.52981 (10274)
  SS BOND              : bond        0.00258 (    2)
  SS BOND              : angle       0.84057 (    4)
  hydrogen bonds       : bond        0.03714 (  346)
  hydrogen bonds       : angle       4.99955 (  993)
  Misc. bond           : bond        0.00068 (    2)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   19 CYS cc_start: 0.6898 (t) cc_final: 0.6689 (p)
REVERT: B   53 ASN cc_start: 0.8685 (t0) cc_final: 0.8353 (t0)
REVERT: A   30 GLN cc_start: 0.8456 (tm-30) cc_final: 0.7996 (tm-30)
REVERT: A  159 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8243 (OUTLIER)
REVERT: A  160 ASN cc_start: 0.7108 (OUTLIER) cc_final: 0.6458 (OUTLIER)
REVERT: A  344 ASP cc_start: 0.8324 (t0) cc_final: 0.8052 (t0)
REVERT: A  648 GLU cc_start: 0.8776 (tt0) cc_final: 0.8131 (tp30)
  outliers start: 15
  outliers final: 10
  residues processed: 83
  average time/residue: 0.5230
  time to fit residues: 46.2997
Evaluate side-chains
  77 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain A residue  160 ASN
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  578 SER
Chi-restraints excluded: chain A residue  590 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 47 optimal weight:    0.2980
   chunk 44 optimal weight:    0.8980
   chunk 82 optimal weight:    0.8980
   chunk 73 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 86 optimal weight:    1.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 160 ASN
A 599 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.099619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.075509 restraints weight = 11725.764|
|-----------------------------------------------------------------------------|
r_work (start): 0.2904 rms_B_bonded: 2.56
r_work: 0.2779 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2645 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.1949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083   7580  Z= 0.141
  Angle     :  0.514   7.442  10278  Z= 0.274
  Chirality :  0.045   0.158   1075
  Planarity :  0.005   0.050   1351
  Dihedral  :  7.108  58.764   1076
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 2.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 18.47 %
    Favored  : 80.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  0.22 (0.28), residues: 900
  helix:  2.48 (0.55), residues: 89
  sheet:  0.62 (0.24), residues: 441
  loop : -1.01 (0.30), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 469 
 TYR   0.015   0.001   TYR C  67 
 PHE   0.012   0.001   PHE A 211 
 TRP   0.008   0.001   TRP A 180 
 HIS   0.003   0.001   HIS A 745 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 7576)
  covalent geometry    : angle       0.51403 (10274)
  SS BOND              : bond        0.00231 (    2)
  SS BOND              : angle       0.77773 (    4)
  hydrogen bonds       : bond        0.03522 (  346)
  hydrogen bonds       : angle       4.94550 (  993)
  Misc. bond           : bond        0.00058 (    2)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   53 ASN cc_start: 0.8695 (t0) cc_final: 0.8364 (t0)
REVERT: A   30 GLN cc_start: 0.8376 (tm-30) cc_final: 0.8009 (tm-30)
REVERT: A  159 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8204 (OUTLIER)
REVERT: A  160 ASN cc_start: 0.7111 (OUTLIER) cc_final: 0.6517 (t0)
REVERT: A  344 ASP cc_start: 0.8316 (t0) cc_final: 0.8056 (t0)
REVERT: A  615 ARG cc_start: 0.8808 (tpt90) cc_final: 0.8114 (tpt90)
REVERT: A  648 GLU cc_start: 0.8787 (tt0) cc_final: 0.8167 (tp30)
  outliers start: 10
  outliers final: 9
  residues processed: 77
  average time/residue: 0.5445
  time to fit residues: 44.7212
Evaluate side-chains
  78 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain A residue  160 ASN
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  578 SER
Chi-restraints excluded: chain A residue  590 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9980
   chunk 81 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9990
   chunk 66 optimal weight:    0.0870
   chunk 11 optimal weight:    0.7980
   chunk 61 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   overall best weight:    0.7360

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

Flipped N/Q/H residues before XYZ refinement:
A 160 ASN
A 599 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.100813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.076744 restraints weight = 11739.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.2947 rms_B_bonded: 2.57
r_work: 0.2840 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2706 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8650
moved from start:          0.2021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083   7580  Z= 0.117
  Angle     :  0.504   8.095  10278  Z= 0.267
  Chirality :  0.045   0.157   1075
  Planarity :  0.005   0.050   1351
  Dihedral  :  6.981  58.507   1076
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 2.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 18.72 %
    Favored  : 80.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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 (0.28), residues: 900
  helix:  2.56 (0.56), residues: 89
  sheet:  0.71 (0.25), residues: 432
  loop : -1.03 (0.30), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 469 
 TYR   0.015   0.001   TYR C  67 
 PHE   0.011   0.001   PHE A 211 
 TRP   0.008   0.001   TRP A 180 
 HIS   0.002   0.001   HIS A 745 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 7576)
  covalent geometry    : angle       0.50411 (10274)
  SS BOND              : bond        0.00205 (    2)
  SS BOND              : angle       0.71956 (    4)
  hydrogen bonds       : bond        0.03305 (  346)
  hydrogen bonds       : angle       4.86801 (  993)
  Misc. bond           : bond        0.00046 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2418.54 seconds
wall clock time: 41 minutes 58.07 seconds (2518.07 seconds total)