Starting phenix.real_space_refine
on Sat May 10 04:51:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iv8_35746/05_2025/8iv8_35746.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iv8_35746/05_2025/8iv8_35746.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.92
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iv8_35746/05_2025/8iv8_35746.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iv8_35746/05_2025/8iv8_35746.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iv8_35746/05_2025/8iv8_35746.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iv8_35746/05_2025/8iv8_35746.cif"
  }
  resolution = 3.92
  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    3137      2.51       5
     N     808      2.21       5
     O     975      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 4944
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "L"
      Number of atoms: 788
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 788
          Classifications: {'peptide': 104}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 100}
    Chain: "H"
      Number of atoms: 918
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 918
          Classifications: {'peptide': 121}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 117}
    Chain: "G"
      Number of atoms: 1435
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 179, 1435
          Classifications: {'peptide': 179}
          Link IDs: {'PTRANS': 9, 'TRANS': 169}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 817
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101}
    Chain: "C"
      Number of atoms: 947
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 947
          Classifications: {'peptide': 119}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 114}
    Chain: "A"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 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: 6.31, per 1000 atoms: 1.28
  Number of scatterers: 4944
  At special positions: 0
  Unit cell: (107.364, 87.914, 69.242, 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     975      8.00
     N     808      7.00
     C    3137      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 336 " - pdb=" SG  CYS G 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 379 " - pdb=" SG  CYS G 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 391 " - pdb=" SG  CYS G 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  23 " - pdb=" SG  CYS D  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " 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 A   1 " - " NAG A   2 "
      " NAG A   2 " - " BMA A   3 "
    NAG-ASN
      " NAG A   1 " - " ASN G 343 "
  Time building additional restraints: 1.26
  Conformation dependent library (CDL) restraints added in 617.6 milliseconds
  

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1150

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 18 sheets defined
      4.6% alpha, 33.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.81
  Creating SS restraints...
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 4.039A  pdb=" N   THR H  31 " --> pdb=" O   SER H  28 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 28 through 32'
    Processing helix  chain 'G' and resid 338 through 343
    Processing helix  chain 'G' and resid 349 through 353
      removed outlier: 3.771A  pdb=" N   TRP G 353 " --> pdb=" O   VAL G 350 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 365 through 370
    Processing helix  chain 'G' and resid 405 through 411
      removed outlier: 4.579A  pdb=" N   ARG G 408 " --> pdb=" O   ASP G 405 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ILE G 410 " --> pdb=" O   VAL G 407 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 5
    Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 12
      removed outlier: 6.608A  pdb=" N   MET L  11 " --> pdb=" O   GLU L 102 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   TRP L  34 " --> pdb=" O   PHE L  46 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'L' and resid 19 through 21
      removed outlier: 3.592A  pdb=" N   ILE L  19 " --> pdb=" O   ILE L  74 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 5
    Processing sheet with id=AA5, first strand: chain 'H' and resid 58 through 59
      removed outlier: 5.873A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 5.844A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ALA H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   SER H  35 " --> pdb=" O   VAL H  97 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ILE H  37 " --> pdb=" O   TYR H  95 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   CYS H  96 " --> pdb=" O   TRP H 111 " (cutoff:3.500A)
      removed outlier: 4.685A  pdb=" N   TRP H 111 " --> pdb=" O   CYS H  96 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   ARG H  98 " --> pdb=" O   ASP H 109 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 58 through 59
      removed outlier: 5.873A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 5.844A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ALA H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   SER H  35 " --> pdb=" O   VAL H  97 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ILE H  37 " --> pdb=" O   TYR H  95 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'G' and resid 357 through 358
      removed outlier: 3.558A  pdb=" N   VAL G 395 " --> pdb=" O   ILE G 358 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'G' and resid 376 through 379
      removed outlier: 3.608A  pdb=" N   ILE G 402 " --> pdb=" O   TYR G 508 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'G' and resid 452 through 454
    Processing sheet with id=AB1, first strand: chain 'D' and resid 5 through 6
      removed outlier: 7.493A  pdb=" N   THR D  69 " --> pdb=" O   ALA D  25 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ILE D  75 " --> pdb=" O   VAL D  19 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 5 through 6
      removed outlier: 7.493A  pdb=" N   THR D  69 " --> pdb=" O   ALA D  25 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   THR D  72 " --> pdb=" O   SER D  65 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   SER D  65 " --> pdb=" O   THR D  72 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 45 through 48
      removed outlier: 7.163A  pdb=" N   TRP D  35 " --> pdb=" O   LEU D  47 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   GLN D  89 " --> pdb=" O   HIS D  34 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   THR D  97 " --> pdb=" O   GLN D  90 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 45 through 48
      removed outlier: 7.163A  pdb=" N   TRP D  35 " --> pdb=" O   LEU D  47 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   GLN D  89 " --> pdb=" O   HIS D  34 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   THR D 102 " --> pdb=" O   TYR D  86 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 4 through 6
      removed outlier: 3.530A  pdb=" N   VAL C  18 " --> pdb=" O   ILE C  83 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 4 through 6
      removed outlier: 3.530A  pdb=" N   VAL C  18 " --> pdb=" O   ILE C  83 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   THR C  78 " --> pdb=" O   GLU C  73 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   GLU C  73 " --> pdb=" O   THR C  78 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 11 through 12
    Processing sheet with id=AB8, first strand: chain 'C' and resid 37 through 39
      removed outlier: 3.596A  pdb=" N   THR C  93 " --> pdb=" O   GLN C  39 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 49 through 51

    133 hydrogen bonds defined for protein.
    315 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: 1.35

  Time building geometry restraints manager: 1.49 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1539
        1.34 -     1.46: 1342
        1.46 -     1.58: 2155
        1.58 -     1.70: 0
        1.70 -     1.82: 33
  Bond restraints: 5069
  Sorted by residual:
  bond pdb=" C   THR D  93 "
       pdb=" N   TRP D  94 "
    ideal  model  delta    sigma   weight residual
    1.331  1.280  0.051 1.59e-02 3.96e+03 1.05e+01
  bond pdb=" C1  BMA A   3 "
       pdb=" C2  BMA A   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.559 -0.040 2.00e-02 2.50e+03 4.07e+00
  bond pdb=" C1  NAG A   2 "
       pdb=" O5  NAG A   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.440 -0.034 2.00e-02 2.50e+03 2.85e+00
  bond pdb=" C1  NAG A   1 "
       pdb=" O5  NAG A   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.80e+00
  bond pdb=" C5  NAG A   2 "
       pdb=" O5  NAG A   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.437 -0.024 2.00e-02 2.50e+03 1.44e+00
  ... (remaining 5064 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.29: 6738
        2.29 -     4.59: 127
        4.59 -     6.88: 15
        6.88 -     9.17: 6
        9.17 -    11.47: 1
  Bond angle restraints: 6887
  Sorted by residual:
  angle pdb=" N   VAL H  48 "
        pdb=" CA  VAL H  48 "
        pdb=" C   VAL H  48 "
      ideal   model   delta    sigma   weight residual
     113.53  109.40    4.13 9.80e-01 1.04e+00 1.78e+01
  angle pdb=" C   SER L  49 "
        pdb=" N   THR L  50 "
        pdb=" CA  THR L  50 "
      ideal   model   delta    sigma   weight residual
     121.54  129.19   -7.65 1.91e+00 2.74e-01 1.60e+01
  angle pdb=" C   SER L  92 "
        pdb=" N   TRP L  93 "
        pdb=" CA  TRP L  93 "
      ideal   model   delta    sigma   weight residual
     121.54  128.99   -7.45 1.91e+00 2.74e-01 1.52e+01
  angle pdb=" C   LEU G 461 "
        pdb=" N   LYS G 462 "
        pdb=" CA  LYS G 462 "
      ideal   model   delta    sigma   weight residual
     120.69  132.16  -11.47 2.95e+00 1.15e-01 1.51e+01
  angle pdb=" C   SER D  40 "
        pdb=" N   HIS D  41 "
        pdb=" CA  HIS D  41 "
      ideal   model   delta    sigma   weight residual
     122.07  127.29   -5.22 1.43e+00 4.89e-01 1.33e+01
  ... (remaining 6882 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.47: 2782
       22.47 -    44.93: 189
       44.93 -    67.40: 9
       67.40 -    89.86: 10
       89.86 -   112.33: 4
  Dihedral angle restraints: 2994
    sinusoidal: 1181
      harmonic: 1813
  Sorted by residual:
  dihedral pdb=" CA  TRP C 104 "
           pdb=" C   TRP C 104 "
           pdb=" N   TYR C 105 "
           pdb=" CA  TYR C 105 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.85   23.15     0      5.00e+00 4.00e-02 2.14e+01
  dihedral pdb=" CB  CYS G 336 "
           pdb=" SG  CYS G 336 "
           pdb=" SG  CYS G 361 "
           pdb=" CB  CYS G 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   57.47   35.53     1      1.00e+01 1.00e-02 1.79e+01
  dihedral pdb=" CA  SER L  92 "
           pdb=" C   SER L  92 "
           pdb=" N   TRP L  93 "
           pdb=" CA  TRP L  93 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.51  -19.49     0      5.00e+00 4.00e-02 1.52e+01
  ... (remaining 2991 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 564
       0.055 -    0.109: 145
       0.109 -    0.164: 39
       0.164 -    0.219: 5
       0.219 -    0.273: 1
  Chirality restraints: 754
  Sorted by residual:
  chirality pdb=" C5  BMA A   3 "
            pdb=" C4  BMA A   3 "
            pdb=" C6  BMA A   3 "
            pdb=" O5  BMA A   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.27 2.00e-01 2.50e+01 1.87e+00
  chirality pdb=" C1  NAG A   2 "
            pdb=" O4  NAG A   1 "
            pdb=" C2  NAG A   2 "
            pdb=" O5  NAG A   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.42    0.02 2.00e-02 2.50e+03 1.27e+00
  chirality pdb=" CB  THR C  91 "
            pdb=" CA  THR C  91 "
            pdb=" OG1 THR C  91 "
            pdb=" CG2 THR C  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.34    0.22 2.00e-01 2.50e+01 1.16e+00
  ... (remaining 751 not shown)

  Planarity restraints: 872
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS G 462 "   -0.036 5.00e-02 4.00e+02   5.48e-02 4.80e+00
        pdb=" N   PRO G 463 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO G 463 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO G 463 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS G 336 "    0.034 5.00e-02 4.00e+02   5.23e-02 4.38e+00
        pdb=" N   PRO G 337 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO G 337 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO G 337 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS H  13 "   -0.032 5.00e-02 4.00e+02   4.85e-02 3.76e+00
        pdb=" N   PRO H  14 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO H  14 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO H  14 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 869 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1348
        2.80 -     3.32: 3976
        3.32 -     3.85: 8028
        3.85 -     4.37: 8639
        4.37 -     4.90: 15466
  Nonbonded interactions: 37457
  Sorted by model distance:
  nonbonded pdb=" OH  TYR H  59 "
            pdb=" OH  TYR H 103 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OG  SER G 349 "
            pdb=" O   LEU G 452 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" O   SER L  62 "
            pdb=" OG1 THR L  73 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" OG1 THR D  14 "
            pdb=" OD2 ASP D  17 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" O   SER H  30 "
            pdb=" OG  SER H  30 "
     model   vdw
     2.307 3.040
  ... (remaining 37452 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.83 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             35.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     16.880
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   55.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6946
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      :  0.005   0.051   5079  Z= 0.222
  Angle     :  0.821  11.467   6910  Z= 0.453
  Chirality :  0.054   0.273    754
  Planarity :  0.006   0.055    871
  Dihedral  : 15.131 112.328   1823
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  7.39 %
    Favored  : 91.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -3.56 (0.29), residues: 618
  helix: -4.87 (0.33), residues: 12
  sheet: -1.93 (0.35), residues: 212
  loop : -2.65 (0.25), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP H  47 
 HIS   0.002   0.001   HIS H  99 
 PHE   0.022   0.002   PHE L  46 
 TYR   0.020   0.002   TYR C 105 
 ARG   0.002   0.000   ARG G 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00455 (    1)
  link_NAG-ASN         : angle       4.20579 (    3)
  link_BETA1-4         : bond        0.01030 (    2)
  link_BETA1-4         : angle       2.10522 (    6)
  hydrogen bonds       : bond        0.29075 (  104)
  hydrogen bonds       : angle      11.50099 (  315)
  SS BOND              : bond        0.00350 (    7)
  SS BOND              : angle       1.34297 (   14)
  covalent geometry    : bond        0.00466 ( 5069)
  covalent geometry    : angle       0.81260 ( 6887)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 204
  time to evaluate  : 0.553 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   17 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8303 (tm-30)
REVERT: L   73 THR cc_start: 0.7646 (p) cc_final: 0.7432 (p)
REVERT: L   81 ASP cc_start: 0.7831 (m-30) cc_final: 0.7278 (m-30)
REVERT: H   19 LYS cc_start: 0.8604 (tttt) cc_final: 0.8383 (tttp)
REVERT: H   27 PHE cc_start: 0.8554 (p90) cc_final: 0.8298 (p90)
REVERT: H   29 PHE cc_start: 0.7968 (t80) cc_final: 0.7722 (t80)
REVERT: H   34 MET cc_start: 0.8570 (mtp) cc_final: 0.6943 (mmt)
REVERT: H   60 TYR cc_start: 0.8774 (m-80) cc_final: 0.8492 (m-10)
REVERT: H   73 ASP cc_start: 0.6767 (t70) cc_final: 0.6461 (t70)
REVERT: H   76 MET cc_start: 0.8241 (ttt) cc_final: 0.7909 (tpt)
REVERT: H   87 ARG cc_start: 0.7942 (mtt90) cc_final: 0.7002 (mpt180)
REVERT: H   97 VAL cc_start: 0.9091 (m) cc_final: 0.8389 (m)
REVERT: G  389 ASP cc_start: 0.7983 (t0) cc_final: 0.7563 (p0)
REVERT: G  458 LYS cc_start: 0.8798 (ttmt) cc_final: 0.8356 (tptt)
REVERT: G  467 ASP cc_start: 0.7512 (p0) cc_final: 0.7192 (p0)
REVERT: D   17 ASP cc_start: 0.5154 (m-30) cc_final: 0.4618 (t70)
REVERT: D   47 LEU cc_start: 0.7765 (mt) cc_final: 0.7539 (mp)
REVERT: D  105 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7586 (tm-30)
REVERT: C    5 VAL cc_start: 0.6889 (p) cc_final: 0.6598 (m)
REVERT: C   12 LYS cc_start: 0.7908 (mmtt) cc_final: 0.7705 (mmtt)
REVERT: C   16 GLU cc_start: 0.7397 (mt-10) cc_final: 0.6726 (mt-10)
REVERT: C   60 TYR cc_start: 0.9017 (m-80) cc_final: 0.8569 (m-10)
REVERT: C   65 ARG cc_start: 0.7769 (ttp-110) cc_final: 0.7500 (mmm160)
REVERT: C   82 LYS cc_start: 0.7994 (tttt) cc_final: 0.7467 (ttmm)
REVERT: C   86 LEU cc_start: 0.7536 (mt) cc_final: 0.7294 (mp)
REVERT: C   87 LYS cc_start: 0.8311 (mttt) cc_final: 0.7922 (ttmm)
REVERT: C  104 TRP cc_start: 0.7882 (m-90) cc_final: 0.7135 (m-90)
  outliers start: 4
  outliers final: 2
  residues processed: 207
  average time/residue: 0.1903
  time to fit residues: 48.4871
Evaluate side-chains
  131 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 129
  time to evaluate  : 0.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   13 VAL
Chi-restraints excluded: chain C residue   51 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    0.6980
   chunk 45 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   overall best weight:    0.8786

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

Flipped N/Q/H residues before XYZ refinement:
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  88 HIS
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  57 ASN
H  99 HIS
G 409 GLN
G 439 ASN
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  92 ASN
** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  35 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.116065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.097994 restraints weight = 9468.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.100639 restraints weight = 5721.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.102475 restraints weight = 4063.784|
|-----------------------------------------------------------------------------|
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3123
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3123 r_free = 0.3123    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3123 r_free = 0.3123    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3123
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.2534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5079  Z= 0.185
  Angle     :  0.656   7.331   6910  Z= 0.345
  Chirality :  0.047   0.190    754
  Planarity :  0.005   0.044    871
  Dihedral  :  8.762  63.678    752
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 18.48 %
    Favored  : 77.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -2.90 (0.32), residues: 618
  helix: -4.45 (0.52), residues: 12
  sheet: -1.63 (0.34), residues: 243
  loop : -2.07 (0.29), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP L  90 
 HIS   0.003   0.002   HIS L  33 
 PHE   0.021   0.002   PHE D  71 
 TYR   0.026   0.002   TYR G 351 
 ARG   0.005   0.001   ARG G 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00089 (    1)
  link_NAG-ASN         : angle       2.67785 (    3)
  link_BETA1-4         : bond        0.00580 (    2)
  link_BETA1-4         : angle       2.79101 (    6)
  hydrogen bonds       : bond        0.04337 (  104)
  hydrogen bonds       : angle       6.90817 (  315)
  SS BOND              : bond        0.00458 (    7)
  SS BOND              : angle       1.87536 (   14)
  covalent geometry    : bond        0.00412 ( 5069)
  covalent geometry    : angle       0.64369 ( 6887)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 139
  time to evaluate  : 0.556 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   19 ILE cc_start: 0.8424 (tp) cc_final: 0.8144 (tp)
REVERT: L   60 ARG cc_start: 0.5902 (ptt90) cc_final: 0.5435 (ptt180)
REVERT: D   17 ASP cc_start: 0.5064 (m-30) cc_final: 0.4667 (t70)
REVERT: D   90 GLN cc_start: 0.8131 (pm20) cc_final: 0.7862 (pm20)
REVERT: C   23 LYS cc_start: 0.8742 (ttmm) cc_final: 0.8258 (ttmm)
  outliers start: 20
  outliers final: 11
  residues processed: 154
  average time/residue: 0.1757
  time to fit residues: 34.1460
Evaluate side-chains
  131 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 120
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   41 THR
Chi-restraints excluded: chain L residue   42 SER
Chi-restraints excluded: chain L residue   46 PHE
Chi-restraints excluded: chain L residue   77 VAL
Chi-restraints excluded: chain G residue  366 SER
Chi-restraints excluded: chain G residue  418 ILE
Chi-restraints excluded: chain D residue   13 VAL
Chi-restraints excluded: chain D residue   21 LEU
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue  115 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 27 optimal weight:    0.0970
   chunk 6 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 1 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 21 optimal weight:    0.5980
   chunk 53 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 409 GLN
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  53 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.116412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.097307 restraints weight = 9875.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.100314 restraints weight = 5534.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.102298 restraints weight = 3790.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.3278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   5079  Z= 0.160
  Angle     :  0.641   7.802   6910  Z= 0.333
  Chirality :  0.045   0.176    754
  Planarity :  0.005   0.055    871
  Dihedral  :  7.255  60.880    752
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 21.07 %
    Favored  : 75.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -2.58 (0.33), residues: 618
  helix: -4.24 (0.60), residues: 13
  sheet: -1.44 (0.34), residues: 245
  loop : -1.82 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 102 
 HIS   0.003   0.002   HIS D  41 
 PHE   0.017   0.001   PHE H  68 
 TYR   0.022   0.002   TYR G 351 
 ARG   0.003   0.001   ARG G 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00079 (    1)
  link_NAG-ASN         : angle       2.42816 (    3)
  link_BETA1-4         : bond        0.00337 (    2)
  link_BETA1-4         : angle       2.53944 (    6)
  hydrogen bonds       : bond        0.03707 (  104)
  hydrogen bonds       : angle       6.08692 (  315)
  SS BOND              : bond        0.00534 (    7)
  SS BOND              : angle       2.24294 (   14)
  covalent geometry    : bond        0.00361 ( 5069)
  covalent geometry    : angle       0.62781 ( 6887)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 132
  time to evaluate  : 0.603 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   17 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8285 (tm-30)
REVERT: L   66 SER cc_start: 0.8782 (p) cc_final: 0.8276 (m)
REVERT: G  389 ASP cc_start: 0.8006 (p0) cc_final: 0.7737 (p0)
REVERT: G  427 ASP cc_start: 0.8400 (m-30) cc_final: 0.7787 (t0)
REVERT: D   17 ASP cc_start: 0.5369 (m-30) cc_final: 0.4849 (t70)
REVERT: C   12 LYS cc_start: 0.8190 (mmtt) cc_final: 0.7947 (mmtt)
REVERT: C   31 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8255 (t0)
REVERT: C   73 GLU cc_start: 0.8039 (pp20) cc_final: 0.7794 (pp20)
  outliers start: 21
  outliers final: 18
  residues processed: 148
  average time/residue: 0.2019
  time to fit residues: 37.9850
Evaluate side-chains
  136 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 117
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   41 THR
Chi-restraints excluded: chain L residue   42 SER
Chi-restraints excluded: chain L residue   46 PHE
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   77 VAL
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   57 ASN
Chi-restraints excluded: chain H residue   84 SER
Chi-restraints excluded: chain H residue  108 MET
Chi-restraints excluded: chain G residue  395 VAL
Chi-restraints excluded: chain G residue  407 VAL
Chi-restraints excluded: chain G residue  409 GLN
Chi-restraints excluded: chain G residue  418 ILE
Chi-restraints excluded: chain G residue  511 VAL
Chi-restraints excluded: chain D residue   42 GLU
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   31 ASP
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue  115 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 1 optimal weight:    7.9990
   chunk 18 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 32 optimal weight:    0.6980
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 409 GLN
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.115617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.096105 restraints weight = 10040.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.098957 restraints weight = 5806.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.100781 restraints weight = 4075.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.3564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   5079  Z= 0.176
  Angle     :  0.631   8.650   6910  Z= 0.327
  Chirality :  0.044   0.166    754
  Planarity :  0.004   0.036    871
  Dihedral  :  6.271  57.822    751
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 21.07 %
    Favored  : 74.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -2.41 (0.33), residues: 618
  helix: -4.00 (0.77), residues: 13
  sheet: -1.30 (0.34), residues: 247
  loop : -1.72 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  36 
 HIS   0.003   0.002   HIS L  88 
 PHE   0.016   0.001   PHE H  68 
 TYR   0.019   0.001   TYR G 351 
 ARG   0.005   0.001   ARG G 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00119 (    1)
  link_NAG-ASN         : angle       2.43119 (    3)
  link_BETA1-4         : bond        0.00474 (    2)
  link_BETA1-4         : angle       2.46701 (    6)
  hydrogen bonds       : bond        0.03577 (  104)
  hydrogen bonds       : angle       5.65103 (  315)
  SS BOND              : bond        0.00315 (    7)
  SS BOND              : angle       2.19745 (   14)
  covalent geometry    : bond        0.00398 ( 5069)
  covalent geometry    : angle       0.61739 ( 6887)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 121
  time to evaluate  : 0.561 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   17 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8287 (tm-30)
REVERT: L   66 SER cc_start: 0.8764 (p) cc_final: 0.8186 (m)
REVERT: H   38 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8418 (ptt180)
REVERT: H   93 MET cc_start: 0.8612 (tpp) cc_final: 0.8070 (ttt)
REVERT: G  389 ASP cc_start: 0.8072 (p0) cc_final: 0.7756 (p0)
REVERT: G  427 ASP cc_start: 0.8384 (m-30) cc_final: 0.7854 (t0)
REVERT: D   17 ASP cc_start: 0.5480 (m-30) cc_final: 0.4894 (t70)
REVERT: D  105 GLU cc_start: 0.6993 (tm-30) cc_final: 0.6413 (tt0)
  outliers start: 25
  outliers final: 19
  residues processed: 141
  average time/residue: 0.1694
  time to fit residues: 30.5553
Evaluate side-chains
  135 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   41 THR
Chi-restraints excluded: chain L residue   42 SER
Chi-restraints excluded: chain L residue   46 PHE
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   77 VAL
Chi-restraints excluded: chain H residue   38 ARG
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   57 ASN
Chi-restraints excluded: chain H residue  108 MET
Chi-restraints excluded: chain G residue  383 SER
Chi-restraints excluded: chain G residue  395 VAL
Chi-restraints excluded: chain G residue  407 VAL
Chi-restraints excluded: chain G residue  418 ILE
Chi-restraints excluded: chain G residue  505 TYR
Chi-restraints excluded: chain G residue  511 VAL
Chi-restraints excluded: chain D residue   42 GLU
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue  115 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 20 optimal weight:    0.6980
   chunk 56 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    1.1388

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

Flipped N/Q/H residues before XYZ refinement:
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 409 GLN
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.113039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.094174 restraints weight = 10034.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.096962 restraints weight = 5662.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.098879 restraints weight = 3929.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.3906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   5079  Z= 0.219
  Angle     :  0.662   9.693   6910  Z= 0.344
  Chirality :  0.045   0.169    754
  Planarity :  0.004   0.036    871
  Dihedral  :  6.030  54.875    751
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  5.55 %
    Allowed  : 21.26 %
    Favored  : 73.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -2.30 (0.33), residues: 618
  helix: -3.66 (0.91), residues: 13
  sheet: -1.17 (0.34), residues: 252
  loop : -1.71 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP L  90 
 HIS   0.003   0.002   HIS L  88 
 PHE   0.019   0.002   PHE H  68 
 TYR   0.018   0.002   TYR G 351 
 ARG   0.006   0.001   ARG G 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00141 (    1)
  link_NAG-ASN         : angle       2.59595 (    3)
  link_BETA1-4         : bond        0.00402 (    2)
  link_BETA1-4         : angle       2.23975 (    6)
  hydrogen bonds       : bond        0.03644 (  104)
  hydrogen bonds       : angle       5.47182 (  315)
  SS BOND              : bond        0.00427 (    7)
  SS BOND              : angle       2.37261 (   14)
  covalent geometry    : bond        0.00502 ( 5069)
  covalent geometry    : angle       0.64900 ( 6887)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 119
  time to evaluate  : 0.594 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   10 ILE cc_start: 0.8403 (mp) cc_final: 0.8193 (mm)
REVERT: L   17 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8259 (tm-30)
REVERT: L   66 SER cc_start: 0.8811 (p) cc_final: 0.8181 (m)
REVERT: H   38 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8301 (ptt-90)
REVERT: H   93 MET cc_start: 0.8661 (tpp) cc_final: 0.8153 (ttt)
REVERT: G  389 ASP cc_start: 0.8059 (p0) cc_final: 0.7733 (p0)
REVERT: G  427 ASP cc_start: 0.8487 (m-30) cc_final: 0.7931 (t0)
REVERT: G  467 ASP cc_start: 0.7561 (p0) cc_final: 0.7242 (p0)
REVERT: D   17 ASP cc_start: 0.5668 (m-30) cc_final: 0.5007 (t70)
REVERT: D  105 GLU cc_start: 0.7087 (tm-30) cc_final: 0.6494 (tt0)
REVERT: C   12 LYS cc_start: 0.8405 (mmtt) cc_final: 0.8129 (tptm)
  outliers start: 30
  outliers final: 22
  residues processed: 140
  average time/residue: 0.1975
  time to fit residues: 34.9559
Evaluate side-chains
  136 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   41 THR
Chi-restraints excluded: chain L residue   42 SER
Chi-restraints excluded: chain L residue   46 PHE
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   77 VAL
Chi-restraints excluded: chain H residue   38 ARG
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   84 SER
Chi-restraints excluded: chain H residue  108 MET
Chi-restraints excluded: chain G residue  395 VAL
Chi-restraints excluded: chain G residue  407 VAL
Chi-restraints excluded: chain G residue  409 GLN
Chi-restraints excluded: chain G residue  415 THR
Chi-restraints excluded: chain G residue  418 ILE
Chi-restraints excluded: chain G residue  468 ILE
Chi-restraints excluded: chain G residue  503 VAL
Chi-restraints excluded: chain G residue  505 TYR
Chi-restraints excluded: chain D residue   42 GLU
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   31 ASP
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue  115 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 4 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 55 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
L  36 GLN
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 409 GLN
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 107 ASN ** 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 = 0.3359 r_free = 0.3359 target = 0.113523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.094519 restraints weight = 9822.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.097273 restraints weight = 5658.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.099196 restraints weight = 3951.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.4065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5079  Z= 0.183
  Angle     :  0.641   9.218   6910  Z= 0.333
  Chirality :  0.045   0.154    754
  Planarity :  0.004   0.037    871
  Dihedral  :  5.822  52.807    751
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 22.00 %
    Favored  : 73.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -2.17 (0.33), residues: 618
  helix: -4.05 (0.69), residues: 19
  sheet: -1.20 (0.33), residues: 260
  loop : -1.41 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 104 
 HIS   0.003   0.001   HIS L  88 
 PHE   0.021   0.002   PHE L  46 
 TYR   0.028   0.001   TYR G 351 
 ARG   0.006   0.001   ARG G 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00199 (    1)
  link_NAG-ASN         : angle       2.41361 (    3)
  link_BETA1-4         : bond        0.00425 (    2)
  link_BETA1-4         : angle       2.07444 (    6)
  hydrogen bonds       : bond        0.03397 (  104)
  hydrogen bonds       : angle       5.35079 (  315)
  SS BOND              : bond        0.00570 (    7)
  SS BOND              : angle       2.71995 (   14)
  covalent geometry    : bond        0.00420 ( 5069)
  covalent geometry    : angle       0.62540 ( 6887)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 117
  time to evaluate  : 0.585 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   10 ILE cc_start: 0.8403 (mp) cc_final: 0.8182 (mm)
REVERT: L   17 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8132 (tm-30)
REVERT: L   48 TYR cc_start: 0.8703 (p90) cc_final: 0.8110 (p90)
REVERT: L   66 SER cc_start: 0.8797 (p) cc_final: 0.8166 (m)
REVERT: H   38 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.8307 (ptt-90)
REVERT: H   93 MET cc_start: 0.8658 (tpp) cc_final: 0.7873 (ttt)
REVERT: G  389 ASP cc_start: 0.8083 (p0) cc_final: 0.7725 (p0)
REVERT: G  427 ASP cc_start: 0.8461 (m-30) cc_final: 0.7920 (t0)
REVERT: G  467 ASP cc_start: 0.7468 (p0) cc_final: 0.7183 (p0)
REVERT: D   17 ASP cc_start: 0.5632 (m-30) cc_final: 0.4990 (t70)
REVERT: D  105 GLU cc_start: 0.6999 (tm-30) cc_final: 0.6448 (tt0)
  outliers start: 27
  outliers final: 23
  residues processed: 135
  average time/residue: 0.1829
  time to fit residues: 31.1436
Evaluate side-chains
  137 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 113
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   41 THR
Chi-restraints excluded: chain L residue   42 SER
Chi-restraints excluded: chain L residue   45 VAL
Chi-restraints excluded: chain L residue   46 PHE
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   77 VAL
Chi-restraints excluded: chain L residue   81 ASP
Chi-restraints excluded: chain H residue   38 ARG
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   84 SER
Chi-restraints excluded: chain H residue  108 MET
Chi-restraints excluded: chain G residue  340 GLU
Chi-restraints excluded: chain G residue  395 VAL
Chi-restraints excluded: chain G residue  407 VAL
Chi-restraints excluded: chain G residue  409 GLN
Chi-restraints excluded: chain G residue  415 THR
Chi-restraints excluded: chain G residue  418 ILE
Chi-restraints excluded: chain G residue  503 VAL
Chi-restraints excluded: chain G residue  505 TYR
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue  115 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 34 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 409 GLN
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.114781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.095571 restraints weight = 9809.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.098343 restraints weight = 5715.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.100228 restraints weight = 4017.982|
|-----------------------------------------------------------------------------|
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8341
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      :  0.004   0.034   5079  Z= 0.178
  Angle     :  0.633   9.044   6910  Z= 0.329
  Chirality :  0.045   0.164    754
  Planarity :  0.004   0.037    871
  Dihedral  :  5.703  51.080    751
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  5.18 %
    Allowed  : 22.18 %
    Favored  : 72.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -2.06 (0.33), residues: 618
  helix: -3.90 (0.72), residues: 19
  sheet: -1.16 (0.33), residues: 260
  loop : -1.33 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP L  90 
 HIS   0.003   0.001   HIS L  88 
 PHE   0.025   0.002   PHE L  46 
 TYR   0.030   0.002   TYR G 351 
 ARG   0.006   0.001   ARG G 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00206 (    1)
  link_NAG-ASN         : angle       2.32022 (    3)
  link_BETA1-4         : bond        0.00443 (    2)
  link_BETA1-4         : angle       1.96566 (    6)
  hydrogen bonds       : bond        0.03379 (  104)
  hydrogen bonds       : angle       5.29683 (  315)
  SS BOND              : bond        0.00527 (    7)
  SS BOND              : angle       2.74136 (   14)
  covalent geometry    : bond        0.00411 ( 5069)
  covalent geometry    : angle       0.61711 ( 6887)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 120
  time to evaluate  : 0.532 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   10 ILE cc_start: 0.8408 (mp) cc_final: 0.8179 (mm)
REVERT: L   17 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8090 (tm-30)
REVERT: L   66 SER cc_start: 0.8820 (p) cc_final: 0.8183 (m)
REVERT: H   38 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8297 (ptt-90)
REVERT: H   93 MET cc_start: 0.8673 (tpp) cc_final: 0.7860 (ttt)
REVERT: G  355 ARG cc_start: 0.8223 (ttm-80) cc_final: 0.7740 (ttt90)
REVERT: G  389 ASP cc_start: 0.8080 (p0) cc_final: 0.7713 (p0)
REVERT: G  403 ARG cc_start: 0.8591 (mtt-85) cc_final: 0.8347 (mtt180)
REVERT: G  427 ASP cc_start: 0.8447 (m-30) cc_final: 0.7924 (t0)
REVERT: G  467 ASP cc_start: 0.7439 (p0) cc_final: 0.7104 (p0)
REVERT: D   17 ASP cc_start: 0.5707 (m-30) cc_final: 0.5067 (t70)
REVERT: D   89 GLN cc_start: 0.8668 (pp30) cc_final: 0.8301 (pp30)
  outliers start: 28
  outliers final: 24
  residues processed: 141
  average time/residue: 0.1813
  time to fit residues: 32.1041
Evaluate side-chains
  141 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 116
  time to evaluate  : 0.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   41 THR
Chi-restraints excluded: chain L residue   42 SER
Chi-restraints excluded: chain L residue   45 VAL
Chi-restraints excluded: chain L residue   46 PHE
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   77 VAL
Chi-restraints excluded: chain L residue   81 ASP
Chi-restraints excluded: chain H residue   29 PHE
Chi-restraints excluded: chain H residue   38 ARG
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   84 SER
Chi-restraints excluded: chain H residue  108 MET
Chi-restraints excluded: chain G residue  340 GLU
Chi-restraints excluded: chain G residue  366 SER
Chi-restraints excluded: chain G residue  395 VAL
Chi-restraints excluded: chain G residue  407 VAL
Chi-restraints excluded: chain G residue  409 GLN
Chi-restraints excluded: chain G residue  418 ILE
Chi-restraints excluded: chain G residue  503 VAL
Chi-restraints excluded: chain G residue  505 TYR
Chi-restraints excluded: chain D residue   98 CYS
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue  115 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 8 optimal weight:    3.9990
   chunk 38 optimal weight:    0.5980
   chunk 57 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 37 optimal weight:    0.5980
   chunk 6 optimal weight:    4.9990
   chunk 32 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 47 optimal weight:    0.6980
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 409 GLN
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  27 GLN
** D  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 107 ASN ** 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 = 0.3378 r_free = 0.3378 target = 0.114893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.096161 restraints weight = 9837.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.098858 restraints weight = 5794.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.100716 restraints weight = 4097.166|
|-----------------------------------------------------------------------------|
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.4260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5079  Z= 0.156
  Angle     :  0.638   8.703   6910  Z= 0.329
  Chirality :  0.044   0.161    754
  Planarity :  0.004   0.048    871
  Dihedral  :  5.563  49.374    751
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 23.48 %
    Favored  : 71.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -1.91 (0.33), residues: 618
  helix: -3.37 (0.94), residues: 19
  sheet: -1.01 (0.34), residues: 258
  loop : -1.29 (0.32), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP L  90 
 HIS   0.003   0.001   HIS D  41 
 PHE   0.022   0.002   PHE L  46 
 TYR   0.030   0.001   TYR G 351 
 ARG   0.006   0.001   ARG G 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00226 (    1)
  link_NAG-ASN         : angle       2.16979 (    3)
  link_BETA1-4         : bond        0.00451 (    2)
  link_BETA1-4         : angle       1.85081 (    6)
  hydrogen bonds       : bond        0.03250 (  104)
  hydrogen bonds       : angle       5.19172 (  315)
  SS BOND              : bond        0.00396 (    7)
  SS BOND              : angle       2.66456 (   14)
  covalent geometry    : bond        0.00361 ( 5069)
  covalent geometry    : angle       0.62392 ( 6887)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 120
  time to evaluate  : 0.565 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   10 ILE cc_start: 0.8435 (mp) cc_final: 0.8200 (mm)
REVERT: L   17 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8041 (tm-30)
REVERT: L   66 SER cc_start: 0.8804 (p) cc_final: 0.8179 (m)
REVERT: H   38 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8307 (ptt-90)
REVERT: H   93 MET cc_start: 0.8666 (tpp) cc_final: 0.8071 (ttt)
REVERT: G  355 ARG cc_start: 0.8213 (ttm-80) cc_final: 0.7759 (ttt90)
REVERT: G  389 ASP cc_start: 0.8037 (p0) cc_final: 0.7681 (p0)
REVERT: G  417 LYS cc_start: 0.9186 (tppt) cc_final: 0.8981 (tppt)
REVERT: G  467 ASP cc_start: 0.7366 (p0) cc_final: 0.7053 (p0)
REVERT: D   17 ASP cc_start: 0.5683 (m-30) cc_final: 0.4990 (t70)
REVERT: D   89 GLN cc_start: 0.8626 (pp30) cc_final: 0.8265 (pp30)
REVERT: D  105 GLU cc_start: 0.7043 (tm-30) cc_final: 0.6449 (tt0)
REVERT: C   12 LYS cc_start: 0.8091 (mmmm) cc_final: 0.7508 (tptm)
  outliers start: 27
  outliers final: 26
  residues processed: 139
  average time/residue: 0.1869
  time to fit residues: 32.5889
Evaluate side-chains
  141 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 114
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   41 THR
Chi-restraints excluded: chain L residue   42 SER
Chi-restraints excluded: chain L residue   46 PHE
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   77 VAL
Chi-restraints excluded: chain L residue   81 ASP
Chi-restraints excluded: chain H residue   29 PHE
Chi-restraints excluded: chain H residue   38 ARG
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   84 SER
Chi-restraints excluded: chain H residue  108 MET
Chi-restraints excluded: chain H residue  117 VAL
Chi-restraints excluded: chain G residue  340 GLU
Chi-restraints excluded: chain G residue  366 SER
Chi-restraints excluded: chain G residue  395 VAL
Chi-restraints excluded: chain G residue  407 VAL
Chi-restraints excluded: chain G residue  409 GLN
Chi-restraints excluded: chain G residue  415 THR
Chi-restraints excluded: chain G residue  418 ILE
Chi-restraints excluded: chain G residue  503 VAL
Chi-restraints excluded: chain G residue  505 TYR
Chi-restraints excluded: chain D residue   98 CYS
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue  115 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 50 optimal weight:    0.5980
   chunk 9 optimal weight:    0.0670
   chunk 54 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 45 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 59 optimal weight:    0.5980
   chunk 26 optimal weight:    0.4980
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 409 GLN
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 101 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.115650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.096103 restraints weight = 9719.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.099044 restraints weight = 5544.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.101072 restraints weight = 3830.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.4334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5079  Z= 0.138
  Angle     :  0.627   8.382   6910  Z= 0.327
  Chirality :  0.044   0.166    754
  Planarity :  0.004   0.061    871
  Dihedral  :  5.462  47.628    751
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  5.91 %
    Allowed  : 23.29 %
    Favored  : 70.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -1.76 (0.34), residues: 618
  helix: -3.32 (0.97), residues: 19
  sheet: -0.91 (0.34), residues: 258
  loop : -1.18 (0.33), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP L  90 
 HIS   0.003   0.001   HIS D  41 
 PHE   0.026   0.001   PHE L  46 
 TYR   0.030   0.001   TYR G 351 
 ARG   0.007   0.001   ARG G 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00256 (    1)
  link_NAG-ASN         : angle       1.96427 (    3)
  link_BETA1-4         : bond        0.00419 (    2)
  link_BETA1-4         : angle       1.76047 (    6)
  hydrogen bonds       : bond        0.03131 (  104)
  hydrogen bonds       : angle       5.13064 (  315)
  SS BOND              : bond        0.00355 (    7)
  SS BOND              : angle       2.64180 (   14)
  covalent geometry    : bond        0.00319 ( 5069)
  covalent geometry    : angle       0.61355 ( 6887)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 117
  time to evaluate  : 0.548 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   10 ILE cc_start: 0.8409 (mp) cc_final: 0.8160 (mm)
REVERT: L   17 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8239 (tm-30)
REVERT: L   66 SER cc_start: 0.8784 (p) cc_final: 0.8188 (m)
REVERT: H   38 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8396 (ptt180)
REVERT: H   93 MET cc_start: 0.8675 (tpp) cc_final: 0.8122 (ttt)
REVERT: G  355 ARG cc_start: 0.8200 (ttm-80) cc_final: 0.7748 (ttt90)
REVERT: G  389 ASP cc_start: 0.8042 (p0) cc_final: 0.7750 (p0)
REVERT: G  417 LYS cc_start: 0.9190 (tppt) cc_final: 0.8977 (tppt)
REVERT: G  467 ASP cc_start: 0.7334 (p0) cc_final: 0.7028 (p0)
REVERT: D   17 ASP cc_start: 0.5698 (m-30) cc_final: 0.5043 (t70)
REVERT: D  105 GLU cc_start: 0.7039 (tm-30) cc_final: 0.6510 (tt0)
  outliers start: 32
  outliers final: 27
  residues processed: 138
  average time/residue: 0.1721
  time to fit residues: 30.1930
Evaluate side-chains
  141 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 113
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   41 THR
Chi-restraints excluded: chain L residue   42 SER
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   77 VAL
Chi-restraints excluded: chain L residue   81 ASP
Chi-restraints excluded: chain L residue   94 THR
Chi-restraints excluded: chain H residue   29 PHE
Chi-restraints excluded: chain H residue   38 ARG
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   84 SER
Chi-restraints excluded: chain H residue  108 MET
Chi-restraints excluded: chain H residue  117 VAL
Chi-restraints excluded: chain G residue  340 GLU
Chi-restraints excluded: chain G residue  395 VAL
Chi-restraints excluded: chain G residue  407 VAL
Chi-restraints excluded: chain G residue  409 GLN
Chi-restraints excluded: chain G residue  415 THR
Chi-restraints excluded: chain G residue  418 ILE
Chi-restraints excluded: chain G residue  503 VAL
Chi-restraints excluded: chain G residue  505 TYR
Chi-restraints excluded: chain G residue  511 VAL
Chi-restraints excluded: chain D residue   75 ILE
Chi-restraints excluded: chain D residue   98 CYS
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue  115 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 52 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0170
   chunk 16 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 46 optimal weight:    0.6980
   overall best weight:    1.1422

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

Flipped N/Q/H residues before XYZ refinement:
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 409 GLN
G 450 ASN
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 101 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.114384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.095311 restraints weight = 9911.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.098133 restraints weight = 5682.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.100063 restraints weight = 3942.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.4479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   5079  Z= 0.219
  Angle     :  0.687   8.338   6910  Z= 0.357
  Chirality :  0.045   0.170    754
  Planarity :  0.005   0.060    871
  Dihedral  :  5.638  48.501    751
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 23.84 %
    Favored  : 70.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -1.81 (0.34), residues: 618
  helix: -3.49 (0.92), residues: 19
  sheet: -0.96 (0.34), residues: 251
  loop : -1.20 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP L  90 
 HIS   0.005   0.002   HIS L  88 
 PHE   0.025   0.002   PHE L  46 
 TYR   0.031   0.001   TYR G 351 
 ARG   0.007   0.001   ARG G 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00152 (    1)
  link_NAG-ASN         : angle       2.33013 (    3)
  link_BETA1-4         : bond        0.00435 (    2)
  link_BETA1-4         : angle       1.86605 (    6)
  hydrogen bonds       : bond        0.03601 (  104)
  hydrogen bonds       : angle       5.22592 (  315)
  SS BOND              : bond        0.00450 (    7)
  SS BOND              : angle       2.72873 (   14)
  covalent geometry    : bond        0.00503 ( 5069)
  covalent geometry    : angle       0.67262 ( 6887)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 113
  time to evaluate  : 0.522 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   10 ILE cc_start: 0.8472 (mp) cc_final: 0.8216 (mm)
REVERT: L   17 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8277 (tm-30)
REVERT: L   66 SER cc_start: 0.8827 (p) cc_final: 0.8207 (m)
REVERT: H   38 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.8291 (ptt-90)
REVERT: H   87 ARG cc_start: 0.7930 (mtt90) cc_final: 0.7278 (mpt-90)
REVERT: H   93 MET cc_start: 0.8686 (tpp) cc_final: 0.8197 (ttt)
REVERT: G  389 ASP cc_start: 0.8033 (p0) cc_final: 0.7777 (p0)
REVERT: G  403 ARG cc_start: 0.8597 (mtt-85) cc_final: 0.8353 (mtt180)
REVERT: G  467 ASP cc_start: 0.7404 (p0) cc_final: 0.7133 (p0)
REVERT: D   17 ASP cc_start: 0.5190 (m-30) cc_final: 0.4570 (t70)
REVERT: D  105 GLU cc_start: 0.7068 (tm-30) cc_final: 0.6531 (tt0)
REVERT: C   94 TYR cc_start: 0.8513 (m-10) cc_final: 0.8230 (m-10)
  outliers start: 29
  outliers final: 27
  residues processed: 136
  average time/residue: 0.1902
  time to fit residues: 32.8103
Evaluate side-chains
  138 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 110
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   41 THR
Chi-restraints excluded: chain L residue   42 SER
Chi-restraints excluded: chain L residue   45 VAL
Chi-restraints excluded: chain L residue   46 PHE
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   77 VAL
Chi-restraints excluded: chain L residue   81 ASP
Chi-restraints excluded: chain L residue   94 THR
Chi-restraints excluded: chain H residue   29 PHE
Chi-restraints excluded: chain H residue   38 ARG
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   84 SER
Chi-restraints excluded: chain H residue  108 MET
Chi-restraints excluded: chain H residue  117 VAL
Chi-restraints excluded: chain G residue  340 GLU
Chi-restraints excluded: chain G residue  395 VAL
Chi-restraints excluded: chain G residue  407 VAL
Chi-restraints excluded: chain G residue  409 GLN
Chi-restraints excluded: chain G residue  418 ILE
Chi-restraints excluded: chain G residue  503 VAL
Chi-restraints excluded: chain G residue  505 TYR
Chi-restraints excluded: chain D residue   75 ILE
Chi-restraints excluded: chain D residue   98 CYS
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue  115 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0980
   chunk 44 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0870
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 409 GLN
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  76 ASN
** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 101 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.116109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.096775 restraints weight = 9809.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.099621 restraints weight = 5644.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.101551 restraints weight = 3939.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.4622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5079  Z= 0.143
  Angle     :  0.662   8.065   6910  Z= 0.341
  Chirality :  0.044   0.167    754
  Planarity :  0.004   0.053    871
  Dihedral  :  5.545  46.858    751
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 24.77 %
    Favored  : 70.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -1.67 (0.34), residues: 618
  helix: -3.48 (0.94), residues: 19
  sheet: -0.77 (0.35), residues: 245
  loop : -1.18 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP L  90 
 HIS   0.004   0.001   HIS D  41 
 PHE   0.022   0.001   PHE L  46 
 TYR   0.030   0.001   TYR G 351 
 ARG   0.007   0.001   ARG G 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00274 (    1)
  link_NAG-ASN         : angle       1.93794 (    3)
  link_BETA1-4         : bond        0.00448 (    2)
  link_BETA1-4         : angle       1.71561 (    6)
  hydrogen bonds       : bond        0.03280 (  104)
  hydrogen bonds       : angle       5.11760 (  315)
  SS BOND              : bond        0.00383 (    7)
  SS BOND              : angle       2.57455 (   14)
  covalent geometry    : bond        0.00329 ( 5069)
  covalent geometry    : angle       0.64980 ( 6887)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2446.72 seconds
wall clock time: 44 minutes 39.96 seconds (2679.96 seconds total)