Starting phenix.real_space_refine
on Fri Jul 25 12:45:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7s05_24784/07_2025/7s05_24784.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7s05_24784/07_2025/7s05_24784.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7s05_24784/07_2025/7s05_24784.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7s05_24784/07_2025/7s05_24784.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7s05_24784/07_2025/7s05_24784.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7s05_24784/07_2025/7s05_24784.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 sd=   0.077
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     S      40      5.16       5
     C    4778      2.51       5
     N    1274      2.21       5
     O    1410      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 7504
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "B"
      Number of atoms: 3653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 437, 3653
          Classifications: {'peptide': 437}
          Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 414}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 3653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 437, 3653
          Classifications: {'peptide': 437}
          Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 414}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 43
          Unusual residues: {' CA': 1, 'NAG': 3}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 43
          Unusual residues: {' CA': 1, 'NAG': 3}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 5.21, per 1000 atoms: 0.69
  Number of scatterers: 7504
  At special positions: 0
  Unit cell: (116.748, 123.372, 72.864, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      2     19.99
     S      40     16.00
     O    1410      8.00
     N    1274      7.00
     C    4778      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  70 " - pdb=" SG  CYS A  70 " 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=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG A1301 " - " ASN A1009 "
      " NAG A1302 " - " ASN A1056 "
      " NAG A1303 " - " ASN A 376 "
      " NAG B1301 " - " ASN B1009 "
      " NAG B1302 " - " ASN B1056 "
      " NAG B1303 " - " ASN B 376 "
      " NAG C   1 " - " ASN B  83 "
      " NAG D   1 " - " ASN B1129 "
      " NAG E   1 " - " ASN A  83 "
      " NAG F   1 " - " ASN A1129 "
  Time building additional restraints: 2.08
  Conformation dependent library (CDL) restraints added in 913.6 milliseconds
  

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1704

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 10 sheets defined
      52.3% alpha, 12.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.96
  Creating SS restraints...
    Processing helix  chain 'B' and resid 49 through 55
    Processing helix  chain 'B' and resid 65 through 70
    Processing helix  chain 'B' and resid 85 through 111
    Processing helix  chain 'B' and resid 327 through 340
      removed outlier: 3.589A  pdb=" N   TYR B 331 " --> pdb=" O   GLU B 327 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 369 through 374
      removed outlier: 3.606A  pdb=" N   VAL B 373 " --> pdb=" O   THR B 369 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 384 through 391
      removed outlier: 4.216A  pdb=" N   HIS B 391 " --> pdb=" O   ALA B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 392 through 395
    Processing helix  chain 'B' and resid 416 through 419
    Processing helix  chain 'B' and resid 931 through 947
    Processing helix  chain 'B' and resid 963 through 973
    Processing helix  chain 'B' and resid 973 through 983
    Processing helix  chain 'B' and resid 993 through 1003
    Processing helix  chain 'B' and resid 1009 through 1018
    Processing helix  chain 'B' and resid 1026 through 1038
    Processing helix  chain 'B' and resid 1043 through 1061
      removed outlier: 3.642A  pdb=" N   LEU B1047 " --> pdb=" O   SER B1043 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1087 through 1094
      removed outlier: 3.634A  pdb=" N   VAL B1091 " --> pdb=" O   THR B1087 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1094 through 1105
    Processing helix  chain 'B' and resid 1129 through 1143
    Processing helix  chain 'B' and resid 1161 through 1176
    Processing helix  chain 'B' and resid 1195 through 1204
    Processing helix  chain 'A' and resid 50 through 55
    Processing helix  chain 'A' and resid 65 through 70
    Processing helix  chain 'A' and resid 85 through 111
    Processing helix  chain 'A' and resid 327 through 340
      removed outlier: 3.591A  pdb=" N   TYR A 331 " --> pdb=" O   GLU A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 374
      removed outlier: 3.605A  pdb=" N   VAL A 373 " --> pdb=" O   THR A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 391
      removed outlier: 4.216A  pdb=" N   HIS A 391 " --> pdb=" O   ALA A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 395
    Processing helix  chain 'A' and resid 416 through 419
    Processing helix  chain 'A' and resid 931 through 947
    Processing helix  chain 'A' and resid 963 through 973
    Processing helix  chain 'A' and resid 973 through 983
    Processing helix  chain 'A' and resid 993 through 1003
    Processing helix  chain 'A' and resid 1009 through 1018
    Processing helix  chain 'A' and resid 1026 through 1038
    Processing helix  chain 'A' and resid 1043 through 1061
      removed outlier: 3.641A  pdb=" N   LEU A1047 " --> pdb=" O   SER A1043 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1087 through 1094
      removed outlier: 3.634A  pdb=" N   VAL A1091 " --> pdb=" O   THR A1087 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1094 through 1105
    Processing helix  chain 'A' and resid 1129 through 1143
    Processing helix  chain 'A' and resid 1161 through 1176
    Processing helix  chain 'A' and resid 1195 through 1204
    Processing sheet with id=AA1, first strand: chain 'B' and resid 365 through 368
      removed outlier: 6.607A  pdb=" N   ILE B 346 " --> pdb=" O   THR B 366 " (cutoff:3.500A)
      removed outlier: 7.297A  pdb=" N   VAL B 368 " --> pdb=" O   ILE B 346 " (cutoff:3.500A)
      removed outlier: 6.082A  pdb=" N   ILE B 348 " --> pdb=" O   VAL B 368 " (cutoff:3.500A)
      removed outlier: 8.739A  pdb=" N   PHE B 347 " --> pdb=" O   ILE B  75 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   VAL B  77 " --> pdb=" O   PHE B 347 " (cutoff:3.500A)
      removed outlier: 7.736A  pdb=" N   VAL B 349 " --> pdb=" O   VAL B  77 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   TYR B  79 " --> pdb=" O   VAL B 349 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   ASP B  76 " --> pdb=" O   ILE B 403 " (cutoff:3.500A)
      removed outlier: 7.370A  pdb=" N   LEU B 405 " --> pdb=" O   ASP B  76 " (cutoff:3.500A)
      removed outlier: 5.942A  pdb=" N   VAL B  78 " --> pdb=" O   LEU B 405 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 409 through 411
      removed outlier: 3.533A  pdb=" N   VAL B1148 " --> pdb=" O   MET B 410 " (cutoff:3.500A)
      removed outlier: 6.015A  pdb=" N   ALA B1122 " --> pdb=" O   CYS B1149 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   ASN B1151 " --> pdb=" O   ALA B1122 " (cutoff:3.500A)
      removed outlier: 7.049A  pdb=" N   LYS B1124 " --> pdb=" O   ASN B1151 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 421 through 422
      removed outlier: 4.142A  pdb=" N   VAL B 953 " --> pdb=" O   THR B 432 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 421 through 422
      removed outlier: 3.632A  pdb=" N   LEU B 431 " --> pdb=" O   MET B1116 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 1005 through 1006
      removed outlier: 3.774A  pdb=" N   GLN B1006 " --> pdb=" O   LYS B1108 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   LYS B1108 " --> pdb=" O   GLN B1006 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 365 through 368
      removed outlier: 6.606A  pdb=" N   ILE A 346 " --> pdb=" O   THR A 366 " (cutoff:3.500A)
      removed outlier: 7.298A  pdb=" N   VAL A 368 " --> pdb=" O   ILE A 346 " (cutoff:3.500A)
      removed outlier: 6.080A  pdb=" N   ILE A 348 " --> pdb=" O   VAL A 368 " (cutoff:3.500A)
      removed outlier: 8.740A  pdb=" N   PHE A 347 " --> pdb=" O   ILE A  75 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   VAL A  77 " --> pdb=" O   PHE A 347 " (cutoff:3.500A)
      removed outlier: 7.736A  pdb=" N   VAL A 349 " --> pdb=" O   VAL A  77 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   TYR A  79 " --> pdb=" O   VAL A 349 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   ASP A  76 " --> pdb=" O   ILE A 403 " (cutoff:3.500A)
      removed outlier: 7.370A  pdb=" N   LEU A 405 " --> pdb=" O   ASP A  76 " (cutoff:3.500A)
      removed outlier: 5.942A  pdb=" N   VAL A  78 " --> pdb=" O   LEU A 405 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 409 through 411
      removed outlier: 3.533A  pdb=" N   VAL A1148 " --> pdb=" O   MET A 410 " (cutoff:3.500A)
      removed outlier: 6.014A  pdb=" N   ALA A1122 " --> pdb=" O   CYS A1149 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   ASN A1151 " --> pdb=" O   ALA A1122 " (cutoff:3.500A)
      removed outlier: 7.048A  pdb=" N   LYS A1124 " --> pdb=" O   ASN A1151 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 421 through 422
      removed outlier: 4.143A  pdb=" N   VAL A 953 " --> pdb=" O   THR A 432 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 421 through 422
      removed outlier: 3.633A  pdb=" N   LEU A 431 " --> pdb=" O   MET A1116 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1005 through 1006
      removed outlier: 3.774A  pdb=" N   GLN A1006 " --> pdb=" O   LYS A1108 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   LYS A1108 " --> pdb=" O   GLN A1006 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1

    317 hydrogen bonds defined for protein.
    921 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.11

  Time building geometry restraints manager: 2.42 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2421
        1.34 -     1.46: 1682
        1.46 -     1.58: 3513
        1.58 -     1.69: 0
        1.69 -     1.81: 72
  Bond restraints: 7688
  Sorted by residual:
  bond pdb=" C1  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.441 -0.035 2.00e-02 2.50e+03 3.06e+00
  bond pdb=" C1  NAG F   2 "
       pdb=" O5  NAG F   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.441 -0.035 2.00e-02 2.50e+03 3.01e+00
  bond pdb=" C1  NAG A1301 "
       pdb=" O5  NAG A1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.440 -0.034 2.00e-02 2.50e+03 2.95e+00
  bond pdb=" C1  NAG B1301 "
       pdb=" O5  NAG B1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.440 -0.034 2.00e-02 2.50e+03 2.93e+00
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.48e+00
  ... (remaining 7683 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 9845
        1.40 -     2.80: 463
        2.80 -     4.21: 70
        4.21 -     5.61: 14
        5.61 -     7.01: 6
  Bond angle restraints: 10398
  Sorted by residual:
  angle pdb=" C   GLU A1118 "
        pdb=" CA  GLU A1118 "
        pdb=" CB  GLU A1118 "
      ideal   model   delta    sigma   weight residual
     111.22  106.92    4.30 1.24e+00 6.50e-01 1.21e+01
  angle pdb=" C   GLU B1118 "
        pdb=" CA  GLU B1118 "
        pdb=" CB  GLU B1118 "
      ideal   model   delta    sigma   weight residual
     111.22  106.96    4.26 1.24e+00 6.50e-01 1.18e+01
  angle pdb=" N   THR B1128 "
        pdb=" CA  THR B1128 "
        pdb=" CB  THR B1128 "
      ideal   model   delta    sigma   weight residual
     112.28  107.19    5.09 1.49e+00 4.50e-01 1.17e+01
  angle pdb=" N   THR A1128 "
        pdb=" CA  THR A1128 "
        pdb=" CB  THR A1128 "
      ideal   model   delta    sigma   weight residual
     112.28  107.24    5.04 1.49e+00 4.50e-01 1.14e+01
  angle pdb=" N   LEU B 380 "
        pdb=" CA  LEU B 380 "
        pdb=" C   LEU B 380 "
      ideal   model   delta    sigma   weight residual
     109.81  115.90   -6.09 2.21e+00 2.05e-01 7.58e+00
  ... (remaining 10393 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.33: 4336
       20.33 -    40.65: 419
       40.65 -    60.98: 40
       60.98 -    81.31: 20
       81.31 -   101.63: 10
  Dihedral angle restraints: 4825
    sinusoidal: 2219
      harmonic: 2606
  Sorted by residual:
  dihedral pdb=" CA  ARG A1127 "
           pdb=" C   ARG A1127 "
           pdb=" N   THR A1128 "
           pdb=" CA  THR A1128 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.03   29.97     0      5.00e+00 4.00e-02 3.59e+01
  dihedral pdb=" CA  ARG B1127 "
           pdb=" C   ARG B1127 "
           pdb=" N   THR B1128 "
           pdb=" CA  THR B1128 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.07   29.93     0      5.00e+00 4.00e-02 3.58e+01
  dihedral pdb=" CA  PRO B 381 "
           pdb=" C   PRO B 381 "
           pdb=" N   THR B 382 "
           pdb=" CA  THR B 382 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.57  -23.43     0      5.00e+00 4.00e-02 2.20e+01
  ... (remaining 4822 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.093: 1078
       0.093 -    0.186: 68
       0.186 -    0.279: 0
       0.279 -    0.372: 2
       0.372 -    0.465: 4
  Chirality restraints: 1152
  Sorted by residual:
  chirality pdb=" C1  NAG A1303 "
            pdb=" ND2 ASN A 376 "
            pdb=" C2  NAG A1303 "
            pdb=" O5  NAG A1303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.93   -0.47 2.00e-01 2.50e+01 5.41e+00
  chirality pdb=" C1  NAG B1303 "
            pdb=" ND2 ASN B 376 "
            pdb=" C2  NAG B1303 "
            pdb=" O5  NAG B1303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.94   -0.46 2.00e-01 2.50e+01 5.34e+00
  chirality pdb=" C1  NAG A1302 "
            pdb=" ND2 ASN A1056 "
            pdb=" C2  NAG A1302 "
            pdb=" O5  NAG A1302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.02   -0.38 2.00e-01 2.50e+01 3.57e+00
  ... (remaining 1149 not shown)

  Planarity restraints: 1336
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 376 "   -0.027 2.00e-02 2.50e+03   2.58e-02 8.33e+00
        pdb=" CG  ASN B 376 "    0.026 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 376 "   -0.003 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 376 "    0.033 2.00e-02 2.50e+03
        pdb=" C1  NAG B1303 "   -0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 376 "    0.027 2.00e-02 2.50e+03   2.58e-02 8.32e+00
        pdb=" CG  ASN A 376 "   -0.026 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 376 "    0.003 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 376 "   -0.033 2.00e-02 2.50e+03
        pdb=" C1  NAG A1303 "    0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B1178 "    0.028 5.00e-02 4.00e+02   4.31e-02 2.97e+00
        pdb=" N   PRO B1179 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO B1179 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B1179 "    0.024 5.00e-02 4.00e+02
  ... (remaining 1333 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 797
        2.75 -     3.29: 7235
        3.29 -     3.82: 12351
        3.82 -     4.36: 14719
        4.36 -     4.90: 25433
  Nonbonded interactions: 60535
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B  79 "
            pdb=" OG  SER B 332 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" OH  TYR A  79 "
            pdb=" OG  SER A 332 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" O   SER B 356 "
            pdb=" NH2 ARG B1186 "
     model   vdw
     2.304 3.120
  nonbonded pdb=" O   SER A 356 "
            pdb=" NH2 ARG A1186 "
     model   vdw
     2.304 3.120
  nonbonded pdb=" OH  TYR A 937 "
            pdb=" OE1 GLU A 976 "
     model   vdw
     2.344 3.040
  ... (remaining 60530 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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:             1.320
  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:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     21.600
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
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   0.053   7703  Z= 0.181
  Angle     :  0.721  10.314  10442  Z= 0.381
  Chirality :  0.052   0.465   1152
  Planarity :  0.004   0.043   1326
  Dihedral  : 16.047 101.632   3118
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.29), residues: 858
  helix:  1.27 (0.26), residues: 394
  sheet:  0.37 (0.55), residues: 98
  loop : -1.39 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1201 
 HIS   0.013   0.001   HIS A 987 
 PHE   0.010   0.001   PHE B1176 
 TYR   0.016   0.001   TYR A 999 
 ARG   0.006   0.000   ARG A1127 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00890 (   10)
  link_NAG-ASN         : angle       4.45648 (   30)
  link_BETA1-4         : bond        0.00799 (    4)
  link_BETA1-4         : angle       1.63571 (   12)
  hydrogen bonds       : bond        0.16026 (  313)
  hydrogen bonds       : angle       6.74831 (  921)
  SS BOND              : bond        0.00430 (    1)
  SS BOND              : angle       2.44459 (    2)
  covalent geometry    : bond        0.00378 ( 7688)
  covalent geometry    : angle       0.67856 (10398)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.789 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.1920
  time to fit residues: 31.2452
Evaluate side-chains
  85 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 65 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 43 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   chunk 67 optimal weight:    0.5980
   chunk 26 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 987 HIS
B1012 GLN
A 987 HIS
A1012 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.176786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.130982 restraints weight = 8031.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.3473 rms_B_bonded: 2.21
r_work: 0.3275 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3112 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.1154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   7703  Z= 0.153
  Angle     :  0.656   7.255  10442  Z= 0.323
  Chirality :  0.051   0.373   1152
  Planarity :  0.004   0.032   1326
  Dihedral  : 10.302  76.151   1250
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  :  7.40 %
    Favored  : 91.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.29), residues: 858
  helix:  1.56 (0.25), residues: 394
  sheet:  0.29 (0.53), residues: 102
  loop : -1.26 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B1201 
 HIS   0.004   0.001   HIS B 423 
 PHE   0.009   0.001   PHE B 411 
 TYR   0.026   0.002   TYR B 999 
 ARG   0.007   0.000   ARG A1127 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00980 (   10)
  link_NAG-ASN         : angle       3.35749 (   30)
  link_BETA1-4         : bond        0.00605 (    4)
  link_BETA1-4         : angle       1.75128 (   12)
  hydrogen bonds       : bond        0.03822 (  313)
  hydrogen bonds       : angle       5.02357 (  921)
  SS BOND              : bond        0.00185 (    1)
  SS BOND              : angle       0.14301 (    2)
  covalent geometry    : bond        0.00360 ( 7688)
  covalent geometry    : angle       0.62909 (10398)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 0.870 
Fit side-chains
REVERT: B  392 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8383 (mt)
REVERT: B 1116 MET cc_start: 0.7990 (mpp) cc_final: 0.7453 (mpp)
REVERT: B 1125 MET cc_start: 0.6596 (tpt) cc_final: 0.6354 (tpt)
REVERT: B 1127 ARG cc_start: 0.8197 (mtt-85) cc_final: 0.7963 (mtt-85)
REVERT: A  392 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8345 (mt)
REVERT: A  975 GLU cc_start: 0.6819 (tm-30) cc_final: 0.6568 (pm20)
REVERT: A 1116 MET cc_start: 0.8030 (mpp) cc_final: 0.7508 (mpp)
REVERT: A 1127 ARG cc_start: 0.8302 (mtt-85) cc_final: 0.8094 (mtt-85)
  outliers start: 13
  outliers final: 8
  residues processed: 118
  average time/residue: 0.2183
  time to fit residues: 34.0712
Evaluate side-chains
  103 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 ASN
Chi-restraints excluded: chain B residue  326 ASN
Chi-restraints excluded: chain B residue  372 ASP
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain B residue 1178 ILE
Chi-restraints excluded: chain A residue  326 ASN
Chi-restraints excluded: chain A residue  372 ASP
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  392 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 68 optimal weight:    0.0170
   chunk 34 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 73 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0670
   chunk 22 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9980
   overall best weight:    0.4956

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

Flipped N/Q/H residues before XYZ refinement:
B 326 ASN
B 987 HIS
A 326 ASN
A 987 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.178193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.130964 restraints weight = 8195.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3522 rms_B_bonded: 2.49
r_work: 0.3336 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3170 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.1492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7703  Z= 0.126
  Angle     :  0.605   7.126  10442  Z= 0.295
  Chirality :  0.048   0.323   1152
  Planarity :  0.004   0.032   1326
  Dihedral  :  9.301  68.863   1250
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  :  9.34 %
    Favored  : 89.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.29), residues: 858
  helix:  1.78 (0.25), residues: 394
  sheet:  0.21 (0.53), residues: 102
  loop : -1.18 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B1201 
 HIS   0.002   0.001   HIS A 423 
 PHE   0.009   0.001   PHE B 931 
 TYR   0.021   0.002   TYR B 999 
 ARG   0.004   0.000   ARG A1127 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00961 (   10)
  link_NAG-ASN         : angle       3.10425 (   30)
  link_BETA1-4         : bond        0.00476 (    4)
  link_BETA1-4         : angle       1.78667 (   12)
  hydrogen bonds       : bond        0.03478 (  313)
  hydrogen bonds       : angle       4.67423 (  921)
  SS BOND              : bond        0.00070 (    1)
  SS BOND              : angle       0.17948 (    2)
  covalent geometry    : bond        0.00289 ( 7688)
  covalent geometry    : angle       0.58004 (10398)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.771 
Fit side-chains
REVERT: A  975 GLU cc_start: 0.6993 (tm-30) cc_final: 0.6695 (pm20)
REVERT: A 1127 ARG cc_start: 0.8289 (mtt-85) cc_final: 0.7969 (mtt180)
  outliers start: 13
  outliers final: 11
  residues processed: 112
  average time/residue: 0.2090
  time to fit residues: 31.3570
Evaluate side-chains
  101 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 ASN
Chi-restraints excluded: chain B residue  326 ASN
Chi-restraints excluded: chain B residue  351 ASN
Chi-restraints excluded: chain B residue  372 ASP
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue 1178 ILE
Chi-restraints excluded: chain A residue  326 ASN
Chi-restraints excluded: chain A residue  351 ASN
Chi-restraints excluded: chain A residue  372 ASP
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue 1178 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 43 optimal weight:    5.9990
   chunk 75 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 5 optimal weight:   10.0000
   chunk 15 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 14 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9980
   chunk 66 optimal weight:    3.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 987 HIS
A 987 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.173289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.129146 restraints weight = 8195.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 2.17
r_work: 0.3277 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.3106 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.1742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070   7703  Z= 0.156
  Angle     :  0.623   7.550  10442  Z= 0.305
  Chirality :  0.049   0.322   1152
  Planarity :  0.004   0.041   1326
  Dihedral  :  8.307  60.546   1250
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 10.92 %
    Favored  : 87.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.29), residues: 858
  helix:  1.81 (0.25), residues: 394
  sheet:  0.47 (0.54), residues: 98
  loop : -1.18 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 357 
 HIS   0.006   0.001   HIS B1158 
 PHE   0.010   0.001   PHE A 998 
 TYR   0.022   0.002   TYR A 999 
 ARG   0.008   0.000   ARG B1127 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00852 (   10)
  link_NAG-ASN         : angle       2.98907 (   30)
  link_BETA1-4         : bond        0.00408 (    4)
  link_BETA1-4         : angle       1.91950 (   12)
  hydrogen bonds       : bond        0.03458 (  313)
  hydrogen bonds       : angle       4.61583 (  921)
  SS BOND              : bond        0.00022 (    1)
  SS BOND              : angle       0.15830 (    2)
  covalent geometry    : bond        0.00375 ( 7688)
  covalent geometry    : angle       0.59981 (10398)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.852 
Fit side-chains
REVERT: A  107 MET cc_start: 0.5285 (mmp) cc_final: 0.4822 (mtt)
REVERT: A  975 GLU cc_start: 0.6979 (tm-30) cc_final: 0.6683 (pm20)
  outliers start: 11
  outliers final: 8
  residues processed: 108
  average time/residue: 0.2049
  time to fit residues: 29.8596
Evaluate side-chains
  98 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 90
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  372 ASP
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  985 VAL
Chi-restraints excluded: chain B residue 1178 ILE
Chi-restraints excluded: chain A residue  372 ASP
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  985 VAL
Chi-restraints excluded: chain A residue 1178 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   chunk 9 optimal weight:    0.0470
   chunk 30 optimal weight:    2.9990
   chunk 83 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   chunk 50 optimal weight:    0.5980
   chunk 64 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 15 optimal weight:    0.0670
   overall best weight:    0.4616

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

Flipped N/Q/H residues before XYZ refinement:
B 326 ASN
B 987 HIS
B1151 ASN
B1158 HIS
A 326 ASN
A 987 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.176468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.132593 restraints weight = 8022.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.3545 rms_B_bonded: 2.16
r_work: 0.3303 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.3132 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   7703  Z= 0.119
  Angle     :  0.593   7.234  10442  Z= 0.290
  Chirality :  0.047   0.302   1152
  Planarity :  0.004   0.034   1326
  Dihedral  :  7.347  52.074   1250
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 11.53 %
    Favored  : 86.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.29), residues: 858
  helix:  2.04 (0.25), residues: 394
  sheet:  0.46 (0.55), residues: 98
  loop : -1.03 (0.34), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B1201 
 HIS   0.007   0.001   HIS B1158 
 PHE   0.009   0.001   PHE B 383 
 TYR   0.019   0.001   TYR A 999 
 ARG   0.008   0.000   ARG B1127 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00858 (   10)
  link_NAG-ASN         : angle       2.76299 (   30)
  link_BETA1-4         : bond        0.00496 (    4)
  link_BETA1-4         : angle       1.91061 (   12)
  hydrogen bonds       : bond        0.03146 (  313)
  hydrogen bonds       : angle       4.48994 (  921)
  SS BOND              : bond        0.00004 (    1)
  SS BOND              : angle       0.18500 (    2)
  covalent geometry    : bond        0.00275 ( 7688)
  covalent geometry    : angle       0.57140 (10398)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 1.090 
Fit side-chains
REVERT: B  107 MET cc_start: 0.5107 (mmp) cc_final: 0.4633 (mtt)
REVERT: A  107 MET cc_start: 0.5337 (mmp) cc_final: 0.4836 (mtt)
REVERT: A  975 GLU cc_start: 0.6927 (tm-30) cc_final: 0.6654 (pm20)
  outliers start: 19
  outliers final: 7
  residues processed: 114
  average time/residue: 0.2907
  time to fit residues: 45.6266
Evaluate side-chains
  96 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 0.946 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  372 ASP
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue 1118 GLU
Chi-restraints excluded: chain B residue 1178 ILE
Chi-restraints excluded: chain A residue  351 ASN
Chi-restraints excluded: chain A residue  372 ASP
Chi-restraints excluded: chain A residue  373 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 59 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 43 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9990
   chunk 66 optimal weight:    5.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
B 987 HIS
B 992 GLN
** B1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 987 HIS
A 992 GLN
A1151 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.174585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.123365 restraints weight = 8140.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 2.27
r_work: 0.3243 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.2180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7703  Z= 0.172
  Angle     :  0.647   8.246  10442  Z= 0.319
  Chirality :  0.049   0.307   1152
  Planarity :  0.004   0.051   1326
  Dihedral  :  6.824  44.405   1250
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 11.65 %
    Favored  : 85.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.29), residues: 858
  helix:  1.99 (0.25), residues: 394
  sheet:  0.19 (0.54), residues: 102
  loop : -1.04 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 357 
 HIS   0.007   0.001   HIS B1158 
 PHE   0.015   0.001   PHE A 998 
 TYR   0.018   0.002   TYR A 999 
 ARG   0.014   0.000   ARG B1127 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00812 (   10)
  link_NAG-ASN         : angle       2.81439 (   30)
  link_BETA1-4         : bond        0.00497 (    4)
  link_BETA1-4         : angle       1.92567 (   12)
  hydrogen bonds       : bond        0.03480 (  313)
  hydrogen bonds       : angle       4.50238 (  921)
  SS BOND              : bond        0.00100 (    1)
  SS BOND              : angle       0.10176 (    2)
  covalent geometry    : bond        0.00414 ( 7688)
  covalent geometry    : angle       0.62659 (10398)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 0.850 
Fit side-chains
REVERT: B  107 MET cc_start: 0.5063 (mmp) cc_final: 0.4600 (mtt)
REVERT: A  107 MET cc_start: 0.5213 (mmp) cc_final: 0.4691 (mtt)
REVERT: A  975 GLU cc_start: 0.6980 (tm-30) cc_final: 0.6774 (pm20)
  outliers start: 21
  outliers final: 13
  residues processed: 110
  average time/residue: 0.2446
  time to fit residues: 36.0973
Evaluate side-chains
  99 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  372 ASP
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  418 ASP
Chi-restraints excluded: chain B residue  985 VAL
Chi-restraints excluded: chain B residue 1116 MET
Chi-restraints excluded: chain B residue 1118 GLU
Chi-restraints excluded: chain B residue 1178 ILE
Chi-restraints excluded: chain A residue  372 ASP
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  985 VAL
Chi-restraints excluded: chain A residue 1116 MET
Chi-restraints excluded: chain A residue 1118 GLU
Chi-restraints excluded: chain A residue 1178 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9990
   chunk 66 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 75 optimal weight:    0.9990
   chunk 70 optimal weight:    0.6980
   chunk 32 optimal weight:    0.8980
   chunk 67 optimal weight:    0.5980
   chunk 68 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 987 HIS
A 987 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.172652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.127959 restraints weight = 8073.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.3495 rms_B_bonded: 2.17
r_work: 0.3242 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.2319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7703  Z= 0.153
  Angle     :  0.642   9.210  10442  Z= 0.312
  Chirality :  0.049   0.300   1152
  Planarity :  0.004   0.071   1326
  Dihedral  :  6.505  38.866   1250
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 12.50 %
    Favored  : 85.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.29), residues: 858
  helix:  1.95 (0.25), residues: 394
  sheet:  0.31 (0.62), residues: 78
  loop : -0.92 (0.33), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 357 
 HIS   0.006   0.001   HIS B1158 
 PHE   0.014   0.001   PHE A 998 
 TYR   0.019   0.002   TYR A 999 
 ARG   0.016   0.000   ARG B1127 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00794 (   10)
  link_NAG-ASN         : angle       2.71819 (   30)
  link_BETA1-4         : bond        0.00478 (    4)
  link_BETA1-4         : angle       1.85039 (   12)
  hydrogen bonds       : bond        0.03302 (  313)
  hydrogen bonds       : angle       4.44837 (  921)
  SS BOND              : bond        0.00077 (    1)
  SS BOND              : angle       0.15842 (    2)
  covalent geometry    : bond        0.00364 ( 7688)
  covalent geometry    : angle       0.62349 (10398)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.846 
Fit side-chains
REVERT: B  107 MET cc_start: 0.5158 (mmp) cc_final: 0.4686 (mtt)
REVERT: B 1127 ARG cc_start: 0.7997 (mtt-85) cc_final: 0.7696 (mpt-90)
REVERT: B 1170 ASP cc_start: 0.7927 (t0) cc_final: 0.7709 (t70)
REVERT: A  107 MET cc_start: 0.5322 (mmp) cc_final: 0.4791 (mtt)
REVERT: A  410 MET cc_start: 0.8552 (mtm) cc_final: 0.8335 (mtp)
REVERT: A  975 GLU cc_start: 0.6984 (tm-30) cc_final: 0.6783 (pm20)
  outliers start: 16
  outliers final: 11
  residues processed: 103
  average time/residue: 0.2228
  time to fit residues: 30.5559
Evaluate side-chains
  99 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  372 ASP
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  418 ASP
Chi-restraints excluded: chain B residue  985 VAL
Chi-restraints excluded: chain B residue 1116 MET
Chi-restraints excluded: chain B residue 1178 ILE
Chi-restraints excluded: chain A residue  372 ASP
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue 1116 MET
Chi-restraints excluded: chain A residue 1118 GLU
Chi-restraints excluded: chain A residue 1178 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 51 optimal weight:    0.5980
   chunk 55 optimal weight:    0.0020
   chunk 52 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 43 optimal weight:    6.9990
   chunk 44 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9980
   chunk 29 optimal weight:    4.9990
   chunk 71 optimal weight:    0.0570
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.4506

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

Flipped N/Q/H residues before XYZ refinement:
B 987 HIS
A 987 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.176831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.130674 restraints weight = 8215.104|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 2.33
r_work: 0.3257 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.2395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7703  Z= 0.117
  Angle     :  0.604   8.631  10442  Z= 0.293
  Chirality :  0.047   0.288   1152
  Planarity :  0.004   0.056   1326
  Dihedral  :  6.062  38.072   1250
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 13.23 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.30), residues: 858
  helix:  2.13 (0.25), residues: 394
  sheet:  0.63 (0.64), residues: 74
  loop : -0.77 (0.33), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 357 
 HIS   0.005   0.001   HIS A1158 
 PHE   0.009   0.001   PHE B 946 
 TYR   0.017   0.001   TYR A 999 
 ARG   0.017   0.000   ARG A1127 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00781 (   10)
  link_NAG-ASN         : angle       2.57833 (   30)
  link_BETA1-4         : bond        0.00453 (    4)
  link_BETA1-4         : angle       1.83663 (   12)
  hydrogen bonds       : bond        0.02990 (  313)
  hydrogen bonds       : angle       4.34992 (  921)
  SS BOND              : bond        0.00041 (    1)
  SS BOND              : angle       0.18768 (    2)
  covalent geometry    : bond        0.00270 ( 7688)
  covalent geometry    : angle       0.58591 (10398)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.803 
Fit side-chains
REVERT: B  107 MET cc_start: 0.5044 (mmp) cc_final: 0.4565 (mtt)
REVERT: B 1170 ASP cc_start: 0.7830 (t0) cc_final: 0.7622 (t70)
REVERT: A  107 MET cc_start: 0.5277 (mmp) cc_final: 0.4735 (mtt)
  outliers start: 13
  outliers final: 12
  residues processed: 106
  average time/residue: 0.2073
  time to fit residues: 29.5840
Evaluate side-chains
  97 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  372 ASP
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  418 ASP
Chi-restraints excluded: chain B residue  941 ILE
Chi-restraints excluded: chain B residue  985 VAL
Chi-restraints excluded: chain B residue 1116 MET
Chi-restraints excluded: chain A residue  372 ASP
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue 1054 LEU
Chi-restraints excluded: chain A residue 1116 MET
Chi-restraints excluded: chain A residue 1118 GLU
Chi-restraints excluded: chain A residue 1178 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 62 optimal weight:    4.9990
   chunk 5 optimal weight:    9.9990
   chunk 77 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 58 optimal weight:    0.3980
   chunk 53 optimal weight:    2.9990
   chunk 43 optimal weight:    6.9990
   chunk 13 optimal weight:    0.0770
   chunk 24 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   overall best weight:    0.6940

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

Flipped N/Q/H residues before XYZ refinement:
B 987 HIS
B 992 GLN
A 987 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.175676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.130390 restraints weight = 8238.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.3519 rms_B_bonded: 2.30
r_work: 0.3255 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.2502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7703  Z= 0.141
  Angle     :  0.623   7.829  10442  Z= 0.307
  Chirality :  0.047   0.289   1152
  Planarity :  0.004   0.086   1326
  Dihedral  :  5.890  37.060   1250
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 13.83 %
    Favored  : 84.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.30), residues: 858
  helix:  2.14 (0.25), residues: 394
  sheet:  0.41 (0.63), residues: 78
  loop : -0.71 (0.34), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 357 
 HIS   0.004   0.001   HIS A1158 
 PHE   0.015   0.001   PHE B 946 
 TYR   0.018   0.002   TYR A 999 
 ARG   0.015   0.000   ARG B1127 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00752 (   10)
  link_NAG-ASN         : angle       2.55554 (   30)
  link_BETA1-4         : bond        0.00441 (    4)
  link_BETA1-4         : angle       1.78456 (   12)
  hydrogen bonds       : bond        0.03231 (  313)
  hydrogen bonds       : angle       4.40420 (  921)
  SS BOND              : bond        0.00045 (    1)
  SS BOND              : angle       0.16030 (    2)
  covalent geometry    : bond        0.00338 ( 7688)
  covalent geometry    : angle       0.60604 (10398)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 1.371 
Fit side-chains
REVERT: B  107 MET cc_start: 0.5005 (mmp) cc_final: 0.4559 (mtt)
REVERT: B 1127 ARG cc_start: 0.7820 (mtt-85) cc_final: 0.7599 (mpt-90)
REVERT: A  107 MET cc_start: 0.5268 (mmp) cc_final: 0.4815 (mtt)
  outliers start: 15
  outliers final: 14
  residues processed: 101
  average time/residue: 0.2333
  time to fit residues: 32.3254
Evaluate side-chains
  101 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  372 ASP
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  418 ASP
Chi-restraints excluded: chain B residue  941 ILE
Chi-restraints excluded: chain B residue  985 VAL
Chi-restraints excluded: chain B residue 1054 LEU
Chi-restraints excluded: chain B residue 1116 MET
Chi-restraints excluded: chain B residue 1178 ILE
Chi-restraints excluded: chain A residue  372 ASP
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue 1054 LEU
Chi-restraints excluded: chain A residue 1116 MET
Chi-restraints excluded: chain A residue 1118 GLU
Chi-restraints excluded: chain A residue 1178 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 55 optimal weight:    0.0270
   chunk 36 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0270
   chunk 37 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 75 optimal weight:    5.9990
   chunk 83 optimal weight:    0.7980
   overall best weight:    0.5096

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

Flipped N/Q/H residues before XYZ refinement:
B 987 HIS
A 987 HIS
A 992 GLN
A1151 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.177921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.131667 restraints weight = 8245.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 2.32
r_work: 0.3267 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.2575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7703  Z= 0.122
  Angle     :  0.594   8.048  10442  Z= 0.292
  Chirality :  0.047   0.278   1152
  Planarity :  0.004   0.079   1326
  Dihedral  :  5.505  35.901   1250
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 13.96 %
    Favored  : 84.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.30), residues: 858
  helix:  2.20 (0.25), residues: 394
  sheet:  0.71 (0.65), residues: 74
  loop : -0.68 (0.34), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 357 
 HIS   0.004   0.001   HIS A1158 
 PHE   0.012   0.001   PHE A 946 
 TYR   0.018   0.001   TYR B 999 
 ARG   0.017   0.000   ARG B1127 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00757 (   10)
  link_NAG-ASN         : angle       2.45470 (   30)
  link_BETA1-4         : bond        0.00524 (    4)
  link_BETA1-4         : angle       1.73809 (   12)
  hydrogen bonds       : bond        0.03038 (  313)
  hydrogen bonds       : angle       4.33379 (  921)
  SS BOND              : bond        0.00020 (    1)
  SS BOND              : angle       0.14712 (    2)
  covalent geometry    : bond        0.00289 ( 7688)
  covalent geometry    : angle       0.57699 (10398)

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

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

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1716 Ramachandran restraints generated.
    858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.873 
Fit side-chains
REVERT: B  107 MET cc_start: 0.4996 (mmp) cc_final: 0.4525 (mtt)
REVERT: A  107 MET cc_start: 0.5253 (mmp) cc_final: 0.4826 (mtt)
  outliers start: 14
  outliers final: 14
  residues processed: 101
  average time/residue: 0.2014
  time to fit residues: 27.6287
Evaluate side-chains
  102 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  372 ASP
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  418 ASP
Chi-restraints excluded: chain B residue  941 ILE
Chi-restraints excluded: chain B residue  985 VAL
Chi-restraints excluded: chain B residue 1054 LEU
Chi-restraints excluded: chain B residue 1116 MET
Chi-restraints excluded: chain B residue 1178 ILE
Chi-restraints excluded: chain A residue  372 ASP
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  941 ILE
Chi-restraints excluded: chain A residue 1054 LEU
Chi-restraints excluded: chain A residue 1116 MET
Chi-restraints excluded: chain A residue 1118 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 4 optimal weight:    0.3980
   chunk 73 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0770
   chunk 81 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 45 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 42 optimal weight:    6.9990
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:
B 987 HIS
A 987 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.177506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.131493 restraints weight = 8152.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 2.22
r_work: 0.3287 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.3118 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.2628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7703  Z= 0.122
  Angle     :  0.595   7.809  10442  Z= 0.295
  Chirality :  0.046   0.277   1152
  Planarity :  0.004   0.091   1326
  Dihedral  :  5.387  35.009   1250
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 13.83 %
    Favored  : 84.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.30), residues: 858
  helix:  2.24 (0.26), residues: 394
  sheet:  0.72 (0.65), residues: 74
  loop : -0.68 (0.34), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 357 
 HIS   0.004   0.001   HIS A1158 
 PHE   0.015   0.001   PHE B 946 
 TYR   0.018   0.001   TYR A 999 
 ARG   0.017   0.000   ARG A1127 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00745 (   10)
  link_NAG-ASN         : angle       2.41966 (   30)
  link_BETA1-4         : bond        0.00515 (    4)
  link_BETA1-4         : angle       1.65950 (   12)
  hydrogen bonds       : bond        0.03131 (  313)
  hydrogen bonds       : angle       4.35860 (  921)
  SS BOND              : bond        0.00018 (    1)
  SS BOND              : angle       0.16129 (    2)
  covalent geometry    : bond        0.00289 ( 7688)
  covalent geometry    : angle       0.57922 (10398)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4665.45 seconds
wall clock time: 82 minutes 16.48 seconds (4936.48 seconds total)