Starting phenix.real_space_refine
on Sun Apr 27 08:10:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8f0h_28757/04_2025/8f0h_28757.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8f0h_28757/04_2025/8f0h_28757.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.18
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8f0h_28757/04_2025/8f0h_28757.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8f0h_28757/04_2025/8f0h_28757.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8f0h_28757/04_2025/8f0h_28757.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8f0h_28757/04_2025/8f0h_28757.cif"
  }
  resolution = 3.18
  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=  -0.000 sd=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      24      5.16       5
     C    3134      2.51       5
     N     839      2.21       5
     O     962      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 4959
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 960
      Number of conformers: 2
      Conformer: "B"
        Number of residues, atoms: 123, 959
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 2, 'TRANS': 120}
          Unresolved chain link angles: 2
          Unresolved chain link dihedrals: 4
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 2
      Conformer: "A"
        Number of residues, atoms: 123, 958
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 2, 'TRANS': 120}
          Unresolved chain link angles: 2
          Unresolved chain link dihedrals: 4
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
          bond proxies already assigned to first conformer: 976
    Chain: "C"
      Number of atoms: 1528
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 193, 1528
          Classifications: {'peptide': 193}
          Link IDs: {'PTRANS': 11, 'TRANS': 181}
    Chain: "D"
      Number of atoms: 754
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 754
          Classifications: {'peptide': 100}
          Link IDs: {'PTRANS': 7, 'TRANS': 92}
    Chain: "H"
      Number of atoms: 887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 887
          Classifications: {'peptide': 114}
          Link IDs: {'PTRANS': 3, 'TRANS': 110}
    Chain: "L"
      Number of atoms: 792
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 792
          Classifications: {'peptide': 104}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 96}
    Chain: "M"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 5.91, per 1000 atoms: 1.19
  Number of scatterers: 4959
  At special positions: 0
  Unit cell: (67.1, 110, 92.4, 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      24     16.00
     O     962      8.00
     N     839      7.00
     C    3134      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03

  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 M   1 " - " NAG M   2 "
    BETA1-6
      " NAG M   1 " - " FUC M   3 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG M   1 " - " ASN C 343 "
  Time building additional restraints: 1.33
  Conformation dependent library (CDL) restraints added in 738.0 milliseconds
  

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1140

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 14 sheets defined
      8.4% alpha, 34.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.70
  Creating SS restraints...
    Processing helix  chain 'B' and resid 28 through 32
      removed outlier: 3.729A  pdb=" N   TYR B  32 " --> pdb=" O   PHE B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 87 through 91
    Processing helix  chain 'C' and resid 338 through 343
    Processing helix  chain 'C' and resid 364 through 371
      removed outlier: 4.453A  pdb=" N   LEU C 368 " --> pdb=" O   ASP C 364 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 385 through 390
      removed outlier: 3.612A  pdb=" N   ASP C 389 " --> pdb=" O   THR C 385 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 405 through 410
      removed outlier: 4.232A  pdb=" N   ARG C 408 " --> pdb=" O   ASP C 405 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 416 through 422
    Processing helix  chain 'H' and resid 86 through 90
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.678A  pdb=" N   ILE L  83 " --> pdb=" O   PRO L  80 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7
      removed outlier: 3.543A  pdb=" N   GLN B   3 " --> pdb=" O   SER B  25 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 57 through 60
      removed outlier: 6.709A  pdb=" N   GLY B  50 " --> pdb=" O   ILE B  58 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   TYR B  60 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 7.329A  pdb=" N   VAL B  48 " --> pdb=" O   TYR B  60 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   TRP B  36 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   GLY B  50 " --> pdb=" O   MET B  34 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   MET B  34 " --> pdb=" O   GLY B  50 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   ALA B  33 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   VAL B  37 " --> pdb=" O   TYR B  95 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 57 through 60
      removed outlier: 6.709A  pdb=" N   GLY B  50 " --> pdb=" O   ILE B  58 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   TYR B  60 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 7.329A  pdb=" N   VAL B  48 " --> pdb=" O   TYR B  60 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   TRP B  36 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   GLY B  50 " --> pdb=" O   MET B  34 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   MET B  34 " --> pdb=" O   GLY B  50 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   ALA B  33 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   VAL B  37 " --> pdb=" O   TYR B  95 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   TYR B  94 " --> pdb=" O   THR B 120 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 354 through 358
      removed outlier: 3.669A  pdb=" N   ASN C 354 " --> pdb=" O   SER C 399 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   CYS C 432 " --> pdb=" O   LEU C 513 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 361 through 362
      removed outlier: 6.382A  pdb=" N   CYS C 361 " --> pdb=" O   CYS C 525 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'C' and resid 452 through 454
    Processing sheet with id=AA7, first strand: chain 'C' and resid 473 through 474
    Processing sheet with id=AA8, first strand: chain 'D' and resid 18 through 23
    Processing sheet with id=AA9, first strand: chain 'D' and resid 44 through 47
      removed outlier: 5.303A  pdb=" N   LEU D  45 " --> pdb=" O   GLN D  36 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   GLN D  36 " --> pdb=" O   LEU D  45 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   ASP D  91 " --> pdb=" O   HIS D  96 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   HIS D  96 " --> pdb=" O   ASP D  91 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 11
      removed outlier: 5.956A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 114 " (cutoff:3.500A)
      removed outlier: 5.909A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.158A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 11
      removed outlier: 5.956A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 114 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 7
      removed outlier: 4.158A  pdb=" N   ASP L  70 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   SER L  67 " --> pdb=" O   ASP L  70 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 53 through 54
      removed outlier: 6.599A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)

    168 hydrogen bonds defined for protein.
    405 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: 1.43

  Time building geometry restraints manager: 1.59 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: 1594
        1.34 -     1.46: 1215
        1.46 -     1.58: 2244
        1.58 -     1.69: 0
        1.69 -     1.81: 31
  Bond restraints: 5084
  Sorted by residual:
  bond pdb=" N   ILE L  75 "
       pdb=" CA  ILE L  75 "
    ideal  model  delta    sigma   weight residual
    1.462  1.493 -0.031 1.17e-02 7.31e+03 6.93e+00
  bond pdb=" N   THR L  72 "
       pdb=" CA  THR L  72 "
    ideal  model  delta    sigma   weight residual
    1.455  1.487 -0.032 1.25e-02 6.40e+03 6.53e+00
  bond pdb=" N   PHE L  73 "
       pdb=" CA  PHE L  73 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.029 1.21e-02 6.83e+03 5.86e+00
  bond pdb=" N   THR L  74 "
       pdb=" CA  THR L  74 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.029 1.19e-02 7.06e+03 5.77e+00
  bond pdb=" N   SER L  77 "
       pdb=" CA  SER L  77 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.029 1.28e-02 6.10e+03 5.16e+00
  ... (remaining 5079 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.07: 6641
        1.07 -     2.14: 196
        2.14 -     3.21: 54
        3.21 -     4.28: 12
        4.28 -     5.35: 5
  Bond angle restraints: 6908
  Sorted by residual:
  angle pdb=" N   PHE C 338 "
        pdb=" CA  PHE C 338 "
        pdb=" C   PHE C 338 "
      ideal   model   delta    sigma   weight residual
     114.56  109.83    4.73 1.27e+00 6.20e-01 1.39e+01
  angle pdb=" C   ASN L  76 "
        pdb=" CA  ASN L  76 "
        pdb=" CB  ASN L  76 "
      ideal   model   delta    sigma   weight residual
     117.23  112.26    4.97 1.36e+00 5.41e-01 1.34e+01
  angle pdb=" N   ILE L  75 "
        pdb=" CA  ILE L  75 "
        pdb=" C   ILE L  75 "
      ideal   model   delta    sigma   weight residual
     113.07  108.17    4.90 1.36e+00 5.41e-01 1.30e+01
  angle pdb=" CA  LEU L  78 "
        pdb=" C   LEU L  78 "
        pdb=" O   LEU L  78 "
      ideal   model   delta    sigma   weight residual
     122.37  118.24    4.13 1.15e+00 7.56e-01 1.29e+01
  angle pdb=" N   VAL B  64 "
        pdb=" CA  VAL B  64 "
        pdb=" C   VAL B  64 "
      ideal   model   delta    sigma   weight residual
     106.21  109.83   -3.62 1.07e+00 8.73e-01 1.15e+01
  ... (remaining 6903 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.94: 2936
       23.94 -    47.88: 66
       47.88 -    71.83: 6
       71.83 -    95.77: 6
       95.77 -   119.71: 1
  Dihedral angle restraints: 3015
    sinusoidal: 1205
      harmonic: 1810
  Sorted by residual:
  dihedral pdb=" CA  ILE L  29 "
           pdb=" C   ILE L  29 "
           pdb=" N   ASN L  30 "
           pdb=" CA  ASN L  30 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.89  -24.11     0      5.00e+00 4.00e-02 2.33e+01
  dihedral pdb=" C2  FUC M   3 "
           pdb=" C1  FUC M   3 "
           pdb=" O5  FUC M   3 "
           pdb=" C5  FUC M   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
      57.68  -62.03  119.71     1      3.00e+01 1.11e-03 1.60e+01
  dihedral pdb=" C1  FUC M   3 "
           pdb=" C5  FUC M   3 "
           pdb=" O5  FUC M   3 "
           pdb=" C4  FUC M   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
      59.12  -34.07   93.19     1      3.00e+01 1.11e-03 1.13e+01
  ... (remaining 3012 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 575
       0.042 -    0.085: 109
       0.085 -    0.127: 54
       0.127 -    0.169: 2
       0.169 -    0.212: 1
  Chirality restraints: 741
  Sorted by residual:
  chirality pdb=" CA  ILE L  75 "
            pdb=" N   ILE L  75 "
            pdb=" C   ILE L  75 "
            pdb=" CB  ILE L  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.12e+00
  chirality pdb=" C1  NAG M   2 "
            pdb=" O4  NAG M   1 "
            pdb=" C2  NAG M   2 "
            pdb=" O5  NAG M   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.38   -0.02 2.00e-02 2.50e+03 9.14e-01
  chirality pdb=" CA  LEU L  78 "
            pdb=" N   LEU L  78 "
            pdb=" C   LEU L  78 "
            pdb=" CB  LEU L  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.65   -0.14 2.00e-01 2.50e+01 4.77e-01
  ... (remaining 738 not shown)

  Planarity restraints: 893
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO L  95 "   -0.029 5.00e-02 4.00e+02   4.36e-02 3.04e+00
        pdb=" N   PRO L  96 "    0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO L  96 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO L  96 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 520 "   -0.025 5.00e-02 4.00e+02   3.71e-02 2.21e+00
        pdb=" N   PRO C 521 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO C 521 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO C 521 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY H 100 "    0.020 5.00e-02 4.00e+02   2.98e-02 1.42e+00
        pdb=" N   PRO H 101 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO H 101 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO H 101 "    0.017 5.00e-02 4.00e+02
  ... (remaining 890 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.78: 1089
        2.78 -     3.31: 4566
        3.31 -     3.84: 8336
        3.84 -     4.37: 10055
        4.37 -     4.90: 17201
  Nonbonded interactions: 41247
  Sorted by model distance:
  nonbonded pdb=" O   ASN C 439 "
            pdb=" OG  SER C 443 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" OH  TYR L  36 "
            pdb=" OE1 GLN L  89 "
     model   vdw
     2.350 3.040
  nonbonded pdb=" OD1 ASP C 364 "
            pdb=" OG  SER C 366 "
     model   vdw
     2.352 3.040
  nonbonded pdb=" OG  SER C 469 "
            pdb=" OE1 GLU C 471 "
     model   vdw
     2.372 3.040
  nonbonded pdb=" O   PHE B  29 "
            pdb=" NH2 ARG B  72 "
     model   vdw
     2.378 3.120
  ... (remaining 41242 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:             5.740
  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:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.210
  Find NCS groups from input model:        0.070
  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:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5095  Z= 0.152
  Angle     :  0.506   5.351   6933  Z= 0.301
  Chirality :  0.040   0.212    741
  Planarity :  0.004   0.044    892
  Dihedral  : 10.682 119.710   1851
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  4.71 %
    Favored  : 94.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.33), residues: 624
  helix: -1.83 (1.16), residues: 21
  sheet:  0.74 (0.40), residues: 176
  loop : -0.84 (0.29), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP H 107 
 HIS   0.001   0.001   HIS D  96 
 PHE   0.006   0.001   PHE H  67 
 TYR   0.018   0.001   TYR L  91 
 ARG   0.002   0.000   ARG C 509 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00196 (    1)
  link_NAG-ASN         : angle       2.09562 (    3)
  link_BETA1-4         : bond        0.00800 (    1)
  link_BETA1-4         : angle       2.58517 (    3)
  hydrogen bonds       : bond        0.26384 (  154)
  hydrogen bonds       : angle      10.71201 (  405)
  link_BETA1-6         : bond        0.00833 (    1)
  link_BETA1-6         : angle       1.98196 (    3)
  SS BOND              : bond        0.00154 (    8)
  SS BOND              : angle       0.51812 (   16)
  covalent geometry    : bond        0.00253 ( 5084)
  covalent geometry    : angle       0.49993 ( 6908)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 180
  time to evaluate  : 0.684 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   13 GLN cc_start: 0.8246 (tp40) cc_final: 0.7954 (mm-40)
REVERT: C  385 THR cc_start: 0.8740 (t) cc_final: 0.8465 (p)
REVERT: D   77 VAL cc_start: 0.6240 (t) cc_final: 0.5985 (p)
REVERT: H   59 TYR cc_start: 0.8847 (m-80) cc_final: 0.8626 (m-80)
REVERT: L   82 ASP cc_start: 0.7534 (m-30) cc_final: 0.6658 (m-30)
  outliers start: 2
  outliers final: 0
  residues processed: 181
  average time/residue: 0.2502
  time to fit residues: 54.3776
Evaluate side-chains
  123 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 46 optimal weight:    0.1980
   chunk 26 optimal weight:    0.7980
   chunk 16 optimal weight:    0.4980
   chunk 31 optimal weight:    0.0050
   chunk 25 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   chunk 18 optimal weight:    0.5980
   chunk 29 optimal weight:    0.5980
   chunk 36 optimal weight:    4.9990
   chunk 56 optimal weight:    0.6980
   overall best weight:    0.3794

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

Flipped N/Q/H residues before XYZ refinement:
** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D   6 GLN
H 104 HIS
L  30 ASN
L  34 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.102836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.080999 restraints weight = 9966.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 3.09
r_work: 0.3057 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3070
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3070 r_free = 0.3070    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3070 r_free = 0.3070    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3070
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.2410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   5095  Z= 0.154
  Angle     :  0.684  10.828   6933  Z= 0.361
  Chirality :  0.045   0.179    741
  Planarity :  0.005   0.046    892
  Dihedral  :  8.379 105.023    760
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 14.50 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -0.72 (0.33), residues: 624
  helix: -2.93 (0.78), residues: 27
  sheet:  0.62 (0.39), residues: 174
  loop : -0.81 (0.29), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 436 
 HIS   0.004   0.001   HIS C 519 
 PHE   0.022   0.001   PHE C 429 
 TYR   0.020   0.002   TYR B  80 
 ARG   0.007   0.001   ARG B  16 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00115 (    1)
  link_NAG-ASN         : angle       1.69202 (    3)
  link_BETA1-4         : bond        0.00649 (    1)
  link_BETA1-4         : angle       2.05557 (    3)
  hydrogen bonds       : bond        0.04899 (  154)
  hydrogen bonds       : angle       7.37593 (  405)
  link_BETA1-6         : bond        0.01151 (    1)
  link_BETA1-6         : angle       2.48736 (    3)
  SS BOND              : bond        0.01113 (    8)
  SS BOND              : angle       2.94381 (   16)
  covalent geometry    : bond        0.00356 ( 5084)
  covalent geometry    : angle       0.66614 ( 6908)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 140
  time to evaluate  : 0.696 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    5 GLN cc_start: 0.7270 (mp10) cc_final: 0.7067 (mp10)
REVERT: B   13 GLN cc_start: 0.8457 (tp40) cc_final: 0.8231 (mm-40)
REVERT: B   95 TYR cc_start: 0.8390 (m-80) cc_final: 0.8033 (m-80)
REVERT: B  118 LYS cc_start: 0.8383 (mmmt) cc_final: 0.8171 (mmmt)
REVERT: C  471 GLU cc_start: 0.8052 (mp0) cc_final: 0.7725 (mp0)
REVERT: D   37 GLN cc_start: 0.7957 (tt0) cc_final: 0.7215 (tt0)
REVERT: D   52 ASP cc_start: 0.7853 (t0) cc_final: 0.7427 (t0)
REVERT: D   73 THR cc_start: 0.8217 (m) cc_final: 0.7863 (p)
REVERT: D   91 ASP cc_start: 0.7555 (t0) cc_final: 0.7301 (t0)
REVERT: L    2 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8673 (mp)
  outliers start: 9
  outliers final: 4
  residues processed: 146
  average time/residue: 0.2494
  time to fit residues: 44.6857
Evaluate side-chains
  130 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 125
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   83 MET
Chi-restraints excluded: chain D residue    6 GLN
Chi-restraints excluded: chain D residue   68 ASN
Chi-restraints excluded: chain D residue   96 HIS
Chi-restraints excluded: chain L residue    2 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 18 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 12 optimal weight:    0.4980
   chunk 33 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0970
   chunk 34 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0980
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
D   6 GLN
H   3 GLN
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.101691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.079758 restraints weight = 10313.577|
|-----------------------------------------------------------------------------|
r_work (start): 0.3168 rms_B_bonded: 3.15
r_work: 0.3039 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3046
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3046 r_free = 0.3046    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3046 r_free = 0.3046    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3046
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.2894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   5095  Z= 0.149
  Angle     :  0.666  10.992   6933  Z= 0.344
  Chirality :  0.045   0.177    741
  Planarity :  0.005   0.047    892
  Dihedral  :  8.000  95.862    760
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 14.88 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -0.90 (0.32), residues: 624
  helix: -2.94 (0.77), residues: 27
  sheet:  0.51 (0.38), residues: 182
  loop : -0.99 (0.29), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  47 
 HIS   0.003   0.001   HIS C 519 
 PHE   0.010   0.001   PHE C 400 
 TYR   0.021   0.002   TYR B  80 
 ARG   0.007   0.001   ARG B  16 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00166 (    1)
  link_NAG-ASN         : angle       1.47310 (    3)
  link_BETA1-4         : bond        0.00923 (    1)
  link_BETA1-4         : angle       2.04575 (    3)
  hydrogen bonds       : bond        0.04024 (  154)
  hydrogen bonds       : angle       6.49213 (  405)
  link_BETA1-6         : bond        0.01184 (    1)
  link_BETA1-6         : angle       3.00541 (    3)
  SS BOND              : bond        0.00796 (    8)
  SS BOND              : angle       3.12191 (   16)
  covalent geometry    : bond        0.00349 ( 5084)
  covalent geometry    : angle       0.64501 ( 6908)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 133
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   13 GLN cc_start: 0.8460 (tp40) cc_final: 0.8235 (mm-40)
REVERT: B   95 TYR cc_start: 0.8323 (m-80) cc_final: 0.7963 (m-80)
REVERT: B  118 LYS cc_start: 0.8469 (mmmt) cc_final: 0.8259 (mmmt)
REVERT: C  471 GLU cc_start: 0.7987 (mp0) cc_final: 0.7629 (mp0)
REVERT: C  478 THR cc_start: 0.8151 (m) cc_final: 0.7933 (p)
REVERT: D   73 THR cc_start: 0.8213 (m) cc_final: 0.7913 (p)
REVERT: D   91 ASP cc_start: 0.7567 (t0) cc_final: 0.7150 (t0)
REVERT: H   13 GLN cc_start: 0.6372 (tp40) cc_final: 0.5913 (mp10)
REVERT: L    2 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8670 (mp)
REVERT: L   27 GLN cc_start: 0.8253 (mt0) cc_final: 0.8046 (mp10)
  outliers start: 16
  outliers final: 10
  residues processed: 141
  average time/residue: 0.3071
  time to fit residues: 54.3317
Evaluate side-chains
  130 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   83 MET
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain D residue   68 ASN
Chi-restraints excluded: chain D residue   96 HIS
Chi-restraints excluded: chain H residue   68 THR
Chi-restraints excluded: chain H residue   75 LYS
Chi-restraints excluded: chain H residue  103 LEU
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   78 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 34 optimal weight:    0.4980
   chunk 14 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 7 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
H   3 GLN
H 104 HIS
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.098449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.076887 restraints weight = 10215.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.3127 rms_B_bonded: 3.04
r_work: 0.2998 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3003
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3003 r_free = 0.3003    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3004 r_free = 0.3004    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3004
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.3246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   5095  Z= 0.210
  Angle     :  0.705  12.612   6933  Z= 0.364
  Chirality :  0.046   0.156    741
  Planarity :  0.005   0.050    892
  Dihedral  :  7.796  88.464    760
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 15.63 %
    Favored  : 80.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -1.08 (0.32), residues: 624
  helix: -3.18 (0.72), residues: 27
  sheet:  0.33 (0.38), residues: 185
  loop : -1.09 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  47 
 HIS   0.003   0.001   HIS C 519 
 PHE   0.012   0.001   PHE H  79 
 TYR   0.025   0.002   TYR B  80 
 ARG   0.007   0.001   ARG L  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00200 (    1)
  link_NAG-ASN         : angle       1.40091 (    3)
  link_BETA1-4         : bond        0.00841 (    1)
  link_BETA1-4         : angle       2.13719 (    3)
  hydrogen bonds       : bond        0.04039 (  154)
  hydrogen bonds       : angle       6.20557 (  405)
  link_BETA1-6         : bond        0.01207 (    1)
  link_BETA1-6         : angle       3.23336 (    3)
  SS BOND              : bond        0.00870 (    8)
  SS BOND              : angle       3.10532 (   16)
  covalent geometry    : bond        0.00496 ( 5084)
  covalent geometry    : angle       0.68510 ( 6908)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 122
  time to evaluate  : 1.114 
Fit side-chains
   revert: symmetry clash
REVERT: B   13 GLN cc_start: 0.8526 (tp40) cc_final: 0.8295 (mm-40)
REVERT: B   30 ASP cc_start: 0.8844 (p0) cc_final: 0.8443 (p0)
REVERT: B   31 ASP cc_start: 0.8891 (t0) cc_final: 0.8278 (m-30)
REVERT: B   87 ARG cc_start: 0.6988 (mtm-85) cc_final: 0.6508 (mtm180)
REVERT: B   90 ASP cc_start: 0.8409 (m-30) cc_final: 0.8034 (m-30)
REVERT: B   95 TYR cc_start: 0.8332 (m-80) cc_final: 0.8048 (m-80)
REVERT: C  386 LYS cc_start: 0.9397 (mmtm) cc_final: 0.9117 (mmtt)
REVERT: C  471 GLU cc_start: 0.8030 (mp0) cc_final: 0.7794 (mp0)
REVERT: C  478 THR cc_start: 0.8194 (m) cc_final: 0.7950 (p)
REVERT: D   34 TRP cc_start: 0.8770 (m100) cc_final: 0.8320 (m100)
REVERT: D   52 ASP cc_start: 0.7927 (m-30) cc_final: 0.7603 (m-30)
REVERT: D   91 ASP cc_start: 0.7653 (t0) cc_final: 0.7203 (t0)
  outliers start: 21
  outliers final: 13
  residues processed: 132
  average time/residue: 0.2299
  time to fit residues: 37.1062
Evaluate side-chains
  127 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   83 MET
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  391 CYS
Chi-restraints excluded: chain D residue    4 LEU
Chi-restraints excluded: chain D residue    6 GLN
Chi-restraints excluded: chain D residue   96 HIS
Chi-restraints excluded: chain H residue   28 ILE
Chi-restraints excluded: chain H residue   64 LYS
Chi-restraints excluded: chain H residue   75 LYS
Chi-restraints excluded: chain H residue  103 LEU
Chi-restraints excluded: chain L residue    5 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0870
   chunk 40 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 34 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
H   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.099895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.077324 restraints weight = 10350.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.3126 rms_B_bonded: 3.19
r_work: 0.2996 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3001
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3001 r_free = 0.3001    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3001 r_free = 0.3001    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.67   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3001
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.3497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   5095  Z= 0.161
  Angle     :  0.671  12.969   6933  Z= 0.344
  Chirality :  0.045   0.184    741
  Planarity :  0.005   0.049    892
  Dihedral  :  7.270  77.310    760
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 17.14 %
    Favored  : 79.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -1.13 (0.32), residues: 624
  helix: -2.92 (0.72), residues: 27
  sheet:  0.30 (0.39), residues: 177
  loop : -1.12 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  47 
 HIS   0.003   0.001   HIS C 519 
 PHE   0.011   0.001   PHE H  79 
 TYR   0.020   0.002   TYR B  80 
 ARG   0.007   0.001   ARG L  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00191 (    1)
  link_NAG-ASN         : angle       1.39183 (    3)
  link_BETA1-4         : bond        0.00888 (    1)
  link_BETA1-4         : angle       2.09814 (    3)
  hydrogen bonds       : bond        0.03620 (  154)
  hydrogen bonds       : angle       5.94502 (  405)
  link_BETA1-6         : bond        0.01389 (    1)
  link_BETA1-6         : angle       3.49991 (    3)
  SS BOND              : bond        0.00599 (    8)
  SS BOND              : angle       2.69224 (   16)
  covalent geometry    : bond        0.00379 ( 5084)
  covalent geometry    : angle       0.65355 ( 6908)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 123
  time to evaluate  : 0.685 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   30 ASP cc_start: 0.8836 (p0) cc_final: 0.8433 (p0)
REVERT: B   31 ASP cc_start: 0.8870 (t0) cc_final: 0.8260 (m-30)
REVERT: B   76 LYS cc_start: 0.9140 (ptpp) cc_final: 0.8778 (ptpp)
REVERT: B   87 ARG cc_start: 0.7298 (mtm-85) cc_final: 0.6740 (mtm180)
REVERT: B   90 ASP cc_start: 0.8288 (m-30) cc_final: 0.7842 (m-30)
REVERT: B   95 TYR cc_start: 0.8276 (m-80) cc_final: 0.8048 (m-80)
REVERT: C  386 LYS cc_start: 0.9487 (mmtm) cc_final: 0.9198 (mmtt)
REVERT: C  471 GLU cc_start: 0.8101 (mp0) cc_final: 0.7821 (mp0)
REVERT: C  478 THR cc_start: 0.8346 (m) cc_final: 0.8117 (p)
REVERT: D   34 TRP cc_start: 0.8709 (m100) cc_final: 0.8249 (m100)
REVERT: D   52 ASP cc_start: 0.8004 (m-30) cc_final: 0.7642 (m-30)
REVERT: D   91 ASP cc_start: 0.7596 (t0) cc_final: 0.7107 (t0)
REVERT: D   95 ASP cc_start: 0.8868 (OUTLIER) cc_final: 0.8499 (t0)
REVERT: H   13 GLN cc_start: 0.6399 (tp40) cc_final: 0.5898 (mp10)
  outliers start: 20
  outliers final: 15
  residues processed: 132
  average time/residue: 0.2651
  time to fit residues: 42.5138
Evaluate side-chains
  131 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   83 MET
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  391 CYS
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain D residue    4 LEU
Chi-restraints excluded: chain D residue    6 GLN
Chi-restraints excluded: chain D residue   74 ILE
Chi-restraints excluded: chain D residue   95 ASP
Chi-restraints excluded: chain D residue   96 HIS
Chi-restraints excluded: chain H residue   28 ILE
Chi-restraints excluded: chain H residue   68 THR
Chi-restraints excluded: chain H residue   75 LYS
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 37 optimal weight:    6.9990
   chunk 7 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 22 optimal weight:    0.8980
   chunk 39 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
H   3 GLN
L  37 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.098543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.076011 restraints weight = 10380.311|
|-----------------------------------------------------------------------------|
r_work (start): 0.3101 rms_B_bonded: 3.17
r_work: 0.2973 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2974
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2974 r_free = 0.2974    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.67   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2974 r_free = 0.2974    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.67   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2974
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.3704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   5095  Z= 0.193
  Angle     :  0.689  12.011   6933  Z= 0.354
  Chirality :  0.046   0.192    741
  Planarity :  0.005   0.051    892
  Dihedral  :  6.872  63.878    760
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 16.95 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -1.16 (0.32), residues: 624
  helix: -2.91 (0.71), residues: 27
  sheet:  0.24 (0.39), residues: 177
  loop : -1.12 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  47 
 HIS   0.003   0.001   HIS C 519 
 PHE   0.011   0.001   PHE C 486 
 TYR   0.023   0.002   TYR B  80 
 ARG   0.008   0.001   ARG L  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00170 (    1)
  link_NAG-ASN         : angle       1.42096 (    3)
  link_BETA1-4         : bond        0.00993 (    1)
  link_BETA1-4         : angle       2.23452 (    3)
  hydrogen bonds       : bond        0.03652 (  154)
  hydrogen bonds       : angle       5.91058 (  405)
  link_BETA1-6         : bond        0.01589 (    1)
  link_BETA1-6         : angle       3.96966 (    3)
  SS BOND              : bond        0.00697 (    8)
  SS BOND              : angle       2.60498 (   16)
  covalent geometry    : bond        0.00453 ( 5084)
  covalent geometry    : angle       0.67153 ( 6908)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 120
  time to evaluate  : 0.602 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   30 ASP cc_start: 0.8827 (p0) cc_final: 0.8599 (p0)
REVERT: B   31 ASP cc_start: 0.8907 (t0) cc_final: 0.8366 (m-30)
REVERT: B   76 LYS cc_start: 0.9135 (ptpp) cc_final: 0.8775 (ptpp)
REVERT: B   87 ARG cc_start: 0.7279 (mtm-85) cc_final: 0.6943 (mtm180)
REVERT: B   90 ASP cc_start: 0.8371 (m-30) cc_final: 0.7875 (m-30)
REVERT: B   95 TYR cc_start: 0.8318 (m-80) cc_final: 0.8110 (m-80)
REVERT: C  471 GLU cc_start: 0.8106 (mp0) cc_final: 0.7764 (mp0)
REVERT: C  478 THR cc_start: 0.8277 (m) cc_final: 0.8054 (p)
REVERT: D    3 GLU cc_start: 0.6314 (OUTLIER) cc_final: 0.6101 (pp20)
REVERT: D   34 TRP cc_start: 0.8773 (m100) cc_final: 0.8295 (m100)
REVERT: D   52 ASP cc_start: 0.8187 (m-30) cc_final: 0.7794 (m-30)
REVERT: D   53 ARG cc_start: 0.8336 (ttm110) cc_final: 0.7956 (ttm110)
REVERT: D   91 ASP cc_start: 0.7622 (t0) cc_final: 0.7108 (t0)
REVERT: D   95 ASP cc_start: 0.8895 (OUTLIER) cc_final: 0.8538 (t0)
REVERT: H   13 GLN cc_start: 0.6508 (tp40) cc_final: 0.5954 (mp10)
REVERT: L   55 GLU cc_start: 0.9013 (tp30) cc_final: 0.8734 (tp30)
REVERT: L   76 ASN cc_start: 0.7696 (t0) cc_final: 0.7468 (t0)
REVERT: L   78 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7880 (tt)
  outliers start: 24
  outliers final: 15
  residues processed: 131
  average time/residue: 0.2420
  time to fit residues: 39.2517
Evaluate side-chains
  132 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   83 MET
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  392 PHE
Chi-restraints excluded: chain C residue  445 VAL
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain D residue    3 GLU
Chi-restraints excluded: chain D residue    4 LEU
Chi-restraints excluded: chain D residue    6 GLN
Chi-restraints excluded: chain D residue   95 ASP
Chi-restraints excluded: chain D residue   96 HIS
Chi-restraints excluded: chain H residue   28 ILE
Chi-restraints excluded: chain H residue   68 THR
Chi-restraints excluded: chain H residue   75 LYS
Chi-restraints excluded: chain H residue  103 LEU
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   78 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 47 optimal weight:    0.0870
   chunk 16 optimal weight:    0.6980
   chunk 30 optimal weight:    6.9990
   chunk 43 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 18 optimal weight:    0.2980
   chunk 48 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.4758

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

Flipped N/Q/H residues before XYZ refinement:
H   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.099257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.077454 restraints weight = 10111.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.3129 rms_B_bonded: 3.06
r_work: 0.2999 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3007
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3007 r_free = 0.3007    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.67   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3007 r_free = 0.3007    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3007
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.3834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   5095  Z= 0.147
  Angle     :  0.672  11.044   6933  Z= 0.342
  Chirality :  0.044   0.172    741
  Planarity :  0.005   0.049    892
  Dihedral  :  6.254  55.473    760
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 17.33 %
    Favored  : 78.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -1.10 (0.32), residues: 624
  helix: -2.92 (0.72), residues: 27
  sheet:  0.24 (0.39), residues: 178
  loop : -1.06 (0.29), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  47 
 HIS   0.003   0.001   HIS C 519 
 PHE   0.010   0.001   PHE H  79 
 TYR   0.023   0.002   TYR B  80 
 ARG   0.008   0.001   ARG L  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00181 (    1)
  link_NAG-ASN         : angle       1.30798 (    3)
  link_BETA1-4         : bond        0.00882 (    1)
  link_BETA1-4         : angle       2.25776 (    3)
  hydrogen bonds       : bond        0.03305 (  154)
  hydrogen bonds       : angle       5.82531 (  405)
  link_BETA1-6         : bond        0.01854 (    1)
  link_BETA1-6         : angle       4.52745 (    3)
  SS BOND              : bond        0.00644 (    8)
  SS BOND              : angle       2.36227 (   16)
  covalent geometry    : bond        0.00345 ( 5084)
  covalent geometry    : angle       0.65462 ( 6908)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 123
  time to evaluate  : 0.771 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   30 ASP cc_start: 0.8811 (p0) cc_final: 0.8584 (p0)
REVERT: B   31 ASP cc_start: 0.8893 (t0) cc_final: 0.8334 (m-30)
REVERT: B   76 LYS cc_start: 0.9168 (ptpp) cc_final: 0.8821 (ptpp)
REVERT: B   87 ARG cc_start: 0.7373 (mtm-85) cc_final: 0.6769 (mtm180)
REVERT: B   90 ASP cc_start: 0.8304 (m-30) cc_final: 0.7742 (m-30)
REVERT: C  471 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7767 (mp0)
REVERT: D    3 GLU cc_start: 0.6270 (OUTLIER) cc_final: 0.6050 (pp20)
REVERT: D   34 TRP cc_start: 0.8748 (m100) cc_final: 0.8278 (m100)
REVERT: D   52 ASP cc_start: 0.8168 (m-30) cc_final: 0.7730 (m-30)
REVERT: D   53 ARG cc_start: 0.8297 (ttm110) cc_final: 0.8004 (ttm110)
REVERT: D   91 ASP cc_start: 0.7585 (t0) cc_final: 0.7071 (t0)
REVERT: D   95 ASP cc_start: 0.8883 (OUTLIER) cc_final: 0.8549 (t0)
REVERT: H   13 GLN cc_start: 0.6731 (tp40) cc_final: 0.6177 (mp10)
REVERT: L   55 GLU cc_start: 0.8992 (tp30) cc_final: 0.8738 (tp30)
REVERT: L   76 ASN cc_start: 0.7738 (t0) cc_final: 0.7511 (t0)
  outliers start: 20
  outliers final: 16
  residues processed: 131
  average time/residue: 0.3039
  time to fit residues: 49.5699
Evaluate side-chains
  136 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 117
  time to evaluate  : 1.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   83 MET
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  391 CYS
Chi-restraints excluded: chain C residue  471 GLU
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain D residue    3 GLU
Chi-restraints excluded: chain D residue    6 GLN
Chi-restraints excluded: chain D residue   74 ILE
Chi-restraints excluded: chain D residue   95 ASP
Chi-restraints excluded: chain D residue   96 HIS
Chi-restraints excluded: chain H residue   28 ILE
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain H residue   68 THR
Chi-restraints excluded: chain H residue   75 LYS
Chi-restraints excluded: chain H residue  103 LEU
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   78 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 37 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0020
   chunk 8 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.8990

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

Flipped N/Q/H residues before XYZ refinement:
D  37 GLN
H   3 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.096569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.074867 restraints weight = 10357.008|
|-----------------------------------------------------------------------------|
r_work (start): 0.3078 rms_B_bonded: 3.03
r_work: 0.2950 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2958
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2958 r_free = 0.2958    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2958 r_free = 0.2958    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2958
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.3978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   5095  Z= 0.212
  Angle     :  0.706  11.308   6933  Z= 0.364
  Chirality :  0.046   0.171    741
  Planarity :  0.006   0.055    892
  Dihedral  :  5.855  55.768    760
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 17.14 %
    Favored  : 78.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -1.23 (0.32), residues: 624
  helix: -2.93 (0.71), residues: 27
  sheet:  0.02 (0.38), residues: 185
  loop : -1.10 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  47 
 HIS   0.004   0.001   HIS H 104 
 PHE   0.012   0.002   PHE H  79 
 TYR   0.024   0.002   TYR B  80 
 ARG   0.009   0.001   ARG C 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00214 (    1)
  link_NAG-ASN         : angle       1.25060 (    3)
  link_BETA1-4         : bond        0.00984 (    1)
  link_BETA1-4         : angle       2.84616 (    3)
  hydrogen bonds       : bond        0.03674 (  154)
  hydrogen bonds       : angle       5.82604 (  405)
  link_BETA1-6         : bond        0.01221 (    1)
  link_BETA1-6         : angle       4.53269 (    3)
  SS BOND              : bond        0.00703 (    8)
  SS BOND              : angle       2.41603 (   16)
  covalent geometry    : bond        0.00499 ( 5084)
  covalent geometry    : angle       0.68851 ( 6908)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 115
  time to evaluate  : 0.625 
Fit side-chains
   revert: symmetry clash
REVERT: B   13 GLN cc_start: 0.7980 (mm-40) cc_final: 0.7553 (mm-40)
REVERT: B   30 ASP cc_start: 0.8792 (p0) cc_final: 0.8551 (p0)
REVERT: B   31 ASP cc_start: 0.8918 (t0) cc_final: 0.8338 (m-30)
REVERT: B   76 LYS cc_start: 0.9176 (ptpp) cc_final: 0.8836 (ptpp)
REVERT: B   87 ARG cc_start: 0.7473 (mtm-85) cc_final: 0.6596 (mtm-85)
REVERT: B   90 ASP cc_start: 0.8420 (m-30) cc_final: 0.7924 (m-30)
REVERT: C  471 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7719 (mp0)
REVERT: D   52 ASP cc_start: 0.8315 (m-30) cc_final: 0.7859 (m-30)
REVERT: D   91 ASP cc_start: 0.7837 (t0) cc_final: 0.7387 (t0)
REVERT: D   95 ASP cc_start: 0.8899 (OUTLIER) cc_final: 0.8577 (t0)
REVERT: H   13 GLN cc_start: 0.6803 (tp40) cc_final: 0.6180 (mp10)
REVERT: L   76 ASN cc_start: 0.7764 (t0) cc_final: 0.7495 (t0)
REVERT: L   78 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7811 (tt)
  outliers start: 22
  outliers final: 15
  residues processed: 124
  average time/residue: 0.2779
  time to fit residues: 41.2793
Evaluate side-chains
  129 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 1.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   83 MET
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  391 CYS
Chi-restraints excluded: chain C residue  392 PHE
Chi-restraints excluded: chain C residue  471 GLU
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain D residue    6 GLN
Chi-restraints excluded: chain D residue   74 ILE
Chi-restraints excluded: chain D residue   95 ASP
Chi-restraints excluded: chain D residue   96 HIS
Chi-restraints excluded: chain H residue   28 ILE
Chi-restraints excluded: chain H residue   68 THR
Chi-restraints excluded: chain H residue   75 LYS
Chi-restraints excluded: chain H residue  103 LEU
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   78 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 38 optimal weight:    0.5980
   chunk 20 optimal weight:    0.7980
   chunk 22 optimal weight:    0.7980
   chunk 47 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 45 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 51 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
H   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.097901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.075381 restraints weight = 10323.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.3091 rms_B_bonded: 3.15
r_work: 0.2963 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2965
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2965 r_free = 0.2965    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2965 r_free = 0.2965    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2965
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.4124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   5095  Z= 0.174
  Angle     :  0.688  10.652   6933  Z= 0.358
  Chirality :  0.045   0.168    741
  Planarity :  0.005   0.052    892
  Dihedral  :  5.427  54.944    760
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 18.46 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -1.19 (0.32), residues: 624
  helix: -2.86 (0.73), residues: 27
  sheet:  0.10 (0.39), residues: 179
  loop : -1.08 (0.29), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  47 
 HIS   0.003   0.001   HIS C 519 
 PHE   0.011   0.001   PHE H  79 
 TYR   0.026   0.002   TYR B  80 
 ARG   0.008   0.001   ARG L  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00357 (    1)
  link_NAG-ASN         : angle       1.36598 (    3)
  link_BETA1-4         : bond        0.00819 (    1)
  link_BETA1-4         : angle       2.91101 (    3)
  hydrogen bonds       : bond        0.03389 (  154)
  hydrogen bonds       : angle       5.78644 (  405)
  link_BETA1-6         : bond        0.00099 (    1)
  link_BETA1-6         : angle       1.54556 (    3)
  SS BOND              : bond        0.00665 (    8)
  SS BOND              : angle       2.28376 (   16)
  covalent geometry    : bond        0.00413 ( 5084)
  covalent geometry    : angle       0.67643 ( 6908)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 124
  time to evaluate  : 0.709 
Fit side-chains
   revert: symmetry clash
REVERT: B   13 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7668 (mm-40)
REVERT: B   30 ASP cc_start: 0.8810 (p0) cc_final: 0.8559 (p0)
REVERT: B   31 ASP cc_start: 0.8919 (t0) cc_final: 0.8331 (m-30)
REVERT: B   76 LYS cc_start: 0.9175 (ptpp) cc_final: 0.8869 (ptpp)
REVERT: B   87 ARG cc_start: 0.7476 (mtm-85) cc_final: 0.6657 (mtm180)
REVERT: B   90 ASP cc_start: 0.8362 (m-30) cc_final: 0.7882 (m-30)
REVERT: C  471 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7691 (mp0)
REVERT: D   52 ASP cc_start: 0.8209 (m-30) cc_final: 0.7782 (m-30)
REVERT: D   91 ASP cc_start: 0.7840 (t0) cc_final: 0.7388 (t0)
REVERT: D   95 ASP cc_start: 0.8898 (OUTLIER) cc_final: 0.8588 (t0)
REVERT: H    3 GLN cc_start: 0.7558 (tt0) cc_final: 0.7314 (tm-30)
REVERT: H   13 GLN cc_start: 0.6803 (tp40) cc_final: 0.6176 (mp10)
REVERT: L   55 GLU cc_start: 0.8994 (tp30) cc_final: 0.8730 (tp30)
REVERT: L   76 ASN cc_start: 0.7930 (t0) cc_final: 0.7712 (t0)
REVERT: L   78 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7860 (tt)
  outliers start: 20
  outliers final: 16
  residues processed: 132
  average time/residue: 0.2400
  time to fit residues: 39.0359
Evaluate side-chains
  133 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 114
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   83 MET
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  391 CYS
Chi-restraints excluded: chain C residue  392 PHE
Chi-restraints excluded: chain C residue  471 GLU
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain D residue    3 GLU
Chi-restraints excluded: chain D residue    6 GLN
Chi-restraints excluded: chain D residue   74 ILE
Chi-restraints excluded: chain D residue   95 ASP
Chi-restraints excluded: chain D residue   96 HIS
Chi-restraints excluded: chain H residue   28 ILE
Chi-restraints excluded: chain H residue   68 THR
Chi-restraints excluded: chain H residue   75 LYS
Chi-restraints excluded: chain H residue  103 LEU
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   78 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 53 optimal weight:    0.0040
   chunk 19 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0570
   chunk 59 optimal weight:    0.6980
   chunk 21 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 38 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.4710

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.098796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.076428 restraints weight = 10265.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.3107 rms_B_bonded: 3.15
r_work: 0.2980 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2987
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2987 r_free = 0.2987    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2987 r_free = 0.2987    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.54   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2987
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.4173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   5095  Z= 0.144
  Angle     :  0.676   9.904   6933  Z= 0.349
  Chirality :  0.044   0.161    741
  Planarity :  0.005   0.051    892
  Dihedral  :  5.384  55.198    760
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 18.64 %
    Favored  : 77.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -1.13 (0.33), residues: 624
  helix: -2.89 (0.73), residues: 27
  sheet:  0.20 (0.39), residues: 179
  loop : -1.07 (0.29), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP D  34 
 HIS   0.002   0.001   HIS C 519 
 PHE   0.011   0.001   PHE H  27 
 TYR   0.026   0.002   TYR B  80 
 ARG   0.009   0.001   ARG L  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00272 (    1)
  link_NAG-ASN         : angle       1.55501 (    3)
  link_BETA1-4         : bond        0.00825 (    1)
  link_BETA1-4         : angle       2.58359 (    3)
  hydrogen bonds       : bond        0.03176 (  154)
  hydrogen bonds       : angle       5.74431 (  405)
  link_BETA1-6         : bond        0.00129 (    1)
  link_BETA1-6         : angle       1.48870 (    3)
  SS BOND              : bond        0.00626 (    8)
  SS BOND              : angle       2.16986 (   16)
  covalent geometry    : bond        0.00341 ( 5084)
  covalent geometry    : angle       0.66497 ( 6908)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 126
  time to evaluate  : 0.604 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   19 ARG cc_start: 0.8860 (ttt90) cc_final: 0.8609 (ttt90)
REVERT: B   30 ASP cc_start: 0.8785 (p0) cc_final: 0.8526 (p0)
REVERT: B   31 ASP cc_start: 0.8968 (t0) cc_final: 0.8307 (m-30)
REVERT: B   76 LYS cc_start: 0.9165 (ptpp) cc_final: 0.8830 (ptpp)
REVERT: B   87 ARG cc_start: 0.7505 (mtm-85) cc_final: 0.7203 (mtm180)
REVERT: B   90 ASP cc_start: 0.8373 (m-30) cc_final: 0.7881 (m-30)
REVERT: C  471 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7673 (mp0)
REVERT: D   52 ASP cc_start: 0.8185 (m-30) cc_final: 0.7780 (m-30)
REVERT: D   91 ASP cc_start: 0.7800 (t0) cc_final: 0.7415 (t0)
REVERT: D   95 ASP cc_start: 0.8897 (OUTLIER) cc_final: 0.8590 (t0)
REVERT: H   13 GLN cc_start: 0.6679 (tp40) cc_final: 0.6075 (mp10)
REVERT: L   55 GLU cc_start: 0.8986 (tp30) cc_final: 0.8737 (tp30)
REVERT: L   76 ASN cc_start: 0.7935 (t0) cc_final: 0.7680 (t0)
REVERT: L   78 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7736 (tt)
  outliers start: 20
  outliers final: 13
  residues processed: 135
  average time/residue: 0.2341
  time to fit residues: 38.5639
Evaluate side-chains
  135 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 119
  time to evaluate  : 0.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   83 MET
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  392 PHE
Chi-restraints excluded: chain C residue  471 GLU
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain D residue   74 ILE
Chi-restraints excluded: chain D residue   95 ASP
Chi-restraints excluded: chain D residue   96 HIS
Chi-restraints excluded: chain H residue   28 ILE
Chi-restraints excluded: chain H residue   68 THR
Chi-restraints excluded: chain H residue   75 LYS
Chi-restraints excluded: chain H residue  103 LEU
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   78 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 4 optimal weight:    0.4980
   chunk 50 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 44 optimal weight:    0.5980
   chunk 34 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B  13 GLN
H   3 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.097796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.075330 restraints weight = 10462.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.3091 rms_B_bonded: 3.17
r_work: 0.2963 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2969
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2969 r_free = 0.2969    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.54   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2969 r_free = 0.2969    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.55   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2969
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.4252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   5095  Z= 0.182
  Angle     :  0.694   9.933   6933  Z= 0.360
  Chirality :  0.045   0.161    741
  Planarity :  0.006   0.057    892
  Dihedral  :  5.492  55.348    760
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 19.77 %
    Favored  : 76.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -1.17 (0.32), residues: 624
  helix: -2.91 (0.72), residues: 27
  sheet:  0.09 (0.39), residues: 180
  loop : -1.05 (0.29), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D  34 
 HIS   0.002   0.001   HIS C 519 
 PHE   0.011   0.001   PHE H  79 
 TYR   0.027   0.002   TYR B  80 
 ARG   0.009   0.001   ARG L  18 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00230 (    1)
  link_NAG-ASN         : angle       1.59944 (    3)
  link_BETA1-4         : bond        0.00909 (    1)
  link_BETA1-4         : angle       2.55304 (    3)
  hydrogen bonds       : bond        0.03412 (  154)
  hydrogen bonds       : angle       5.76590 (  405)
  link_BETA1-6         : bond        0.00085 (    1)
  link_BETA1-6         : angle       1.37037 (    3)
  SS BOND              : bond        0.00629 (    8)
  SS BOND              : angle       2.27039 (   16)
  covalent geometry    : bond        0.00432 ( 5084)
  covalent geometry    : angle       0.68313 ( 6908)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4295.65 seconds
wall clock time: 78 minutes 17.98 seconds (4697.98 seconds total)