Starting phenix.real_space_refine
on Thu Jul 24 03:49:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iv4_35740/07_2025/8iv4_35740.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iv4_35740/07_2025/8iv4_35740.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iv4_35740/07_2025/8iv4_35740.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iv4_35740/07_2025/8iv4_35740.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iv4_35740/07_2025/8iv4_35740.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iv4_35740/07_2025/8iv4_35740.cif"
  }
  resolution = 3.59
  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=   0.013
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      33      5.16       5
     C    3173      2.51       5
     N     841      2.21       5
     O     980      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 5027
  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: "B"
      Number of atoms: 836
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 836
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 102}
    Chain: "A"
      Number of atoms: 921
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 921
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 2, 'TRANS': 115}
    Chain: "G"
      Number of atoms: 1536
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1536
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 10, 'TRANS': 183}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 7.59, per 1000 atoms: 1.51
  Number of scatterers: 5027
  At special positions: 0
  Unit cell: (86.358, 66.908, 109.698, 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      33     16.00
     O     980      8.00
     N     841      7.00
     C    3173      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, 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 B  23 " - pdb=" SG  CYS B  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  98 " 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 G 480 " - pdb=" SG  CYS G 488 " 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 C   1 " - " NAG C   2 "
    NAG-ASN
      " NAG C   1 " - " ASN G 343 "
  Time building additional restraints: 1.18
  Conformation dependent library (CDL) restraints added in 636.8 milliseconds
  

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1172

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 12 sheets defined
      6.2% alpha, 33.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 4.002A  pdb=" N   THR H  31 " --> pdb=" O   SER H  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 83
      removed outlier: 3.801A  pdb=" N   ASP B  82 " --> pdb=" O   GLN B  79 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   LEU B  83 " --> pdb=" O   CYS B  80 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 79 through 83'
    Processing helix  chain 'A' and resid 53 through 57
    Processing helix  chain 'G' and resid 349 through 353
      removed outlier: 3.918A  pdb=" N   TRP G 353 " --> pdb=" O   VAL G 350 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 364 through 370
      removed outlier: 3.923A  pdb=" N   LEU G 368 " --> pdb=" O   ASP G 364 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 405 through 410
      removed outlier: 4.482A  pdb=" N   ARG G 408 " --> pdb=" O   ASP G 405 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ILE G 410 " --> pdb=" O   VAL G 407 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 416 through 422
      removed outlier: 3.698A  pdb=" N   TYR G 421 " --> pdb=" O   LYS G 417 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7
      removed outlier: 3.745A  pdb=" N   SER L   7 " --> pdb=" O   THR L  22 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   THR L  22 " --> pdb=" O   SER L   7 " (cutoff:3.500A)
      removed outlier: 5.821A  pdb=" N   THR L  68 " --> pdb=" O   VAL L  25 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.532A  pdb=" N   GLU L 102 " --> pdb=" O   MET L  11 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'L' and resid 52 through 53
      removed outlier: 3.560A  pdb=" N   TYR L  48 " --> pdb=" O   ASN L  52 " (cutoff:3.500A)
      removed outlier: 5.417A  pdb=" N   VAL L  45 " --> pdb=" O   GLN L  36 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   GLN L  36 " --> pdb=" O   VAL L  45 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6
      removed outlier: 3.521A  pdb=" N   VAL H   5 " --> pdb=" O   ALA H  23 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ASP H  73 " --> pdb=" O   THR H  78 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.535A  pdb=" N   VAL H  12 " --> pdb=" O   THR H 118 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   THR H 115 " --> pdb=" O   TYR H  94 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   TYR H  94 " --> pdb=" O   THR H 115 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ALA H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 5.811A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.720A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   THR H  40 " --> pdb=" O   LEU H  45 " (cutoff:3.500A)
      removed outlier: 6.077A  pdb=" N   LEU H  45 " --> pdb=" O   THR H  40 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.535A  pdb=" N   VAL H  12 " --> pdb=" O   THR H 118 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   THR H 115 " --> pdb=" O   TYR H  94 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   TYR H  94 " --> pdb=" O   THR H 115 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   TYR H 110 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 5
    Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 12
      removed outlier: 3.565A  pdb=" N   GLU B 105 " --> pdb=" O   MET B  11 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   VAL B  33 " --> pdb=" O   TYR B  49 " (cutoff:3.500A)
      removed outlier: 4.921A  pdb=" N   TYR B  49 " --> pdb=" O   VAL B  33 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   TRP B  35 " --> pdb=" O   MET B  47 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 3 through 6
    Processing sheet with id=AB1, first strand: chain 'A' and resid 10 through 12
      removed outlier: 3.519A  pdb=" N   GLY A  10 " --> pdb=" O   SER A 114 " (cutoff:3.500A)
      removed outlier: 6.876A  pdb=" N   MET A  34 " --> pdb=" O   GLN A  50 " (cutoff:3.500A)
      removed outlier: 4.782A  pdb=" N   GLN A  50 " --> pdb=" O   MET A  34 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   TRP A  36 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'G' and resid 354 through 358
    Processing sheet with id=AB3, first strand: chain 'G' and resid 452 through 454

    146 hydrogen bonds defined for protein.
    357 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: 1.42

  Time building geometry restraints manager: 1.44 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: 1593
        1.34 -     1.46: 1294
        1.46 -     1.58: 2212
        1.58 -     1.69: 0
        1.69 -     1.81: 48
  Bond restraints: 5147
  Sorted by residual:
  bond pdb=" C   LEU G 335 "
       pdb=" N   CYS G 336 "
    ideal  model  delta    sigma   weight residual
    1.331  1.269  0.062 2.07e-02 2.33e+03 8.86e+00
  bond pdb=" C1  NAG C   1 "
       pdb=" O5  NAG C   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.457 -0.051 2.00e-02 2.50e+03 6.54e+00
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.451 -0.045 2.00e-02 2.50e+03 4.97e+00
  bond pdb=" N   TYR G 473 "
       pdb=" CA  TYR G 473 "
    ideal  model  delta    sigma   weight residual
    1.457  1.484 -0.027 1.29e-02 6.01e+03 4.31e+00
  bond pdb=" N   CYS G 488 "
       pdb=" CA  CYS G 488 "
    ideal  model  delta    sigma   weight residual
    1.457  1.480 -0.023 1.29e-02 6.01e+03 3.10e+00
  ... (remaining 5142 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 6609
        1.69 -     3.39: 323
        3.39 -     5.08: 29
        5.08 -     6.77: 10
        6.77 -     8.47: 4
  Bond angle restraints: 6975
  Sorted by residual:
  angle pdb=" C   SER L  49 "
        pdb=" N   THR L  50 "
        pdb=" CA  THR L  50 "
      ideal   model   delta    sigma   weight residual
     121.54  129.08   -7.54 1.91e+00 2.74e-01 1.56e+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  128.98   -7.44 1.91e+00 2.74e-01 1.52e+01
  angle pdb=" N   TYR B  94 "
        pdb=" CA  TYR B  94 "
        pdb=" C   TYR B  94 "
      ideal   model   delta    sigma   weight residual
     109.81  118.28   -8.47 2.21e+00 2.05e-01 1.47e+01
  angle pdb=" C   GLN L  89 "
        pdb=" N   TRP L  90 "
        pdb=" CA  TRP L  90 "
      ideal   model   delta    sigma   weight residual
     120.63  126.24   -5.61 1.61e+00 3.86e-01 1.21e+01
  angle pdb=" N   GLN A 111 "
        pdb=" CA  GLN A 111 "
        pdb=" C   GLN A 111 "
      ideal   model   delta    sigma   weight residual
     114.56  110.26    4.30 1.27e+00 6.20e-01 1.14e+01
  ... (remaining 6970 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 2744
       17.91 -    35.81: 253
       35.81 -    53.72: 45
       53.72 -    71.62: 4
       71.62 -    89.53: 5
  Dihedral angle restraints: 3051
    sinusoidal: 1201
      harmonic: 1850
  Sorted by residual:
  dihedral pdb=" CA  ASN G 487 "
           pdb=" C   ASN G 487 "
           pdb=" N   CYS G 488 "
           pdb=" CA  CYS G 488 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -131.59  -48.41     0      5.00e+00 4.00e-02 9.38e+01
  dihedral pdb=" CA  CYS G 361 "
           pdb=" C   CYS G 361 "
           pdb=" N   VAL G 362 "
           pdb=" CA  VAL G 362 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.79   22.21     0      5.00e+00 4.00e-02 1.97e+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   58.47   34.53     1      1.00e+01 1.00e-02 1.69e+01
  ... (remaining 3048 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 514
       0.047 -    0.094: 171
       0.094 -    0.141: 56
       0.141 -    0.188: 9
       0.188 -    0.235: 4
  Chirality restraints: 754
  Sorted by residual:
  chirality pdb=" CB  VAL H  48 "
            pdb=" CA  VAL H  48 "
            pdb=" CG1 VAL H  48 "
            pdb=" CG2 VAL H  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.38e+00
  chirality pdb=" CB  THR A  28 "
            pdb=" CA  THR A  28 "
            pdb=" OG1 THR A  28 "
            pdb=" CG2 THR A  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.33    0.22 2.00e-01 2.50e+01 1.19e+00
  chirality pdb=" CA  TYR B  94 "
            pdb=" N   TYR B  94 "
            pdb=" C   TYR B  94 "
            pdb=" CB  TYR B  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.14e+00
  ... (remaining 751 not shown)

  Planarity restraints: 892
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN G 487 "    0.016 2.00e-02 2.50e+03   3.17e-02 1.01e+01
        pdb=" C   ASN G 487 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   ASN G 487 "    0.021 2.00e-02 2.50e+03
        pdb=" N   CYS G 488 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B  94 "   -0.046 5.00e-02 4.00e+02   6.91e-02 7.63e+00
        pdb=" N   PRO B  95 "    0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO B  95 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B  95 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA G 520 "    0.042 5.00e-02 4.00e+02   6.33e-02 6.40e+00
        pdb=" N   PRO G 521 "   -0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO G 521 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO G 521 "    0.035 5.00e-02 4.00e+02
  ... (remaining 889 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.83: 1626
        2.83 -     3.35: 3861
        3.35 -     3.87: 8003
        3.87 -     4.38: 8760
        4.38 -     4.90: 16095
  Nonbonded interactions: 38345
  Sorted by model distance:
  nonbonded pdb=" O   SER G 438 "
            pdb=" OG  SER G 438 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" O   SER H  30 "
            pdb=" OG  SER H  30 "
     model   vdw
     2.327 3.040
  nonbonded pdb=" OH  TYR H  59 "
            pdb=" OH  TYR H 103 "
     model   vdw
     2.336 3.040
  nonbonded pdb=" O   ARG H  67 "
            pdb=" OG  SER H  84 "
     model   vdw
     2.354 3.040
  nonbonded pdb=" OG  SER G 438 "
            pdb=" OD2 ASP G 442 "
     model   vdw
     2.361 3.040
  ... (remaining 38340 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:             77.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     20.460
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  101.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6501
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   0.062   5157  Z= 0.258
  Angle     :  0.853   8.871   6997  Z= 0.495
  Chirality :  0.054   0.235    754
  Planarity :  0.007   0.069    891
  Dihedral  : 14.005  89.529   1855
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  6.96 %
    Favored  : 92.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -4.00 (0.27), residues: 634
  helix: -4.95 (0.21), residues: 21
  sheet: -1.94 (0.31), residues: 250
  loop : -3.14 (0.24), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP H  47 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.022   0.002   PHE L  46 
 TYR   0.026   0.002   TYR B  94 
 ARG   0.001   0.000   ARG G 408 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00084 (    1)
  link_NAG-ASN         : angle       6.51442 (    3)
  link_BETA1-4         : bond        0.01097 (    1)
  link_BETA1-4         : angle       1.24981 (    3)
  hydrogen bonds       : bond        0.27686 (  144)
  hydrogen bonds       : angle      10.62234 (  357)
  SS BOND              : bond        0.00296 (    8)
  SS BOND              : angle       0.84826 (   16)
  covalent geometry    : bond        0.00550 ( 5147)
  covalent geometry    : angle       0.84205 ( 6975)

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

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

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 127
  time to evaluate  : 0.507 
Fit side-chains
REVERT: L   11 MET cc_start: 0.7400 (mtt) cc_final: 0.6839 (mtt)
REVERT: L   19 ILE cc_start: 0.8245 (tt) cc_final: 0.8027 (tt)
REVERT: L   32 MET cc_start: 0.7935 (tpp) cc_final: 0.7538 (tpp)
REVERT: L   90 TRP cc_start: 0.7295 (t60) cc_final: 0.7030 (t60)
REVERT: H    3 MET cc_start: 0.6729 (mtm) cc_final: 0.5999 (tpt)
REVERT: H   19 LYS cc_start: 0.7516 (tttt) cc_final: 0.7029 (tttm)
REVERT: H   82 GLN cc_start: 0.7352 (pp30) cc_final: 0.7110 (pp30)
REVERT: H   93 MET cc_start: 0.6589 (ttm) cc_final: 0.6235 (ttm)
REVERT: H  109 ASP cc_start: 0.8068 (m-30) cc_final: 0.7447 (m-30)
REVERT: B    1 ASP cc_start: 0.7827 (p0) cc_final: 0.7625 (p0)
REVERT: B    4 MET cc_start: 0.6457 (mmm) cc_final: 0.5943 (mmt)
REVERT: B   47 MET cc_start: 0.7245 (mmp) cc_final: 0.6926 (mmp)
REVERT: B   52 SER cc_start: 0.8365 (t) cc_final: 0.8140 (m)
REVERT: B   54 ARG cc_start: 0.8177 (ttm110) cc_final: 0.7763 (ttp80)
REVERT: B   79 GLN cc_start: 0.7684 (mm-40) cc_final: 0.7432 (mm110)
REVERT: B   82 ASP cc_start: 0.8596 (m-30) cc_final: 0.8362 (m-30)
REVERT: A   18 MET cc_start: 0.6312 (ttm) cc_final: 0.6019 (ttt)
REVERT: A   19 LYS cc_start: 0.7633 (tttt) cc_final: 0.6874 (tttp)
REVERT: A   35 ASP cc_start: 0.6952 (m-30) cc_final: 0.6541 (m-30)
REVERT: A   50 GLN cc_start: 0.7547 (tt0) cc_final: 0.6930 (tt0)
REVERT: A   69 ARG cc_start: 0.7395 (mtm110) cc_final: 0.7149 (mtp180)
REVERT: A  108 PHE cc_start: 0.7478 (t80) cc_final: 0.7176 (t80)
REVERT: G  347 PHE cc_start: 0.8147 (m-10) cc_final: 0.7861 (m-80)
REVERT: G  369 TYR cc_start: 0.8841 (t80) cc_final: 0.8477 (t80)
REVERT: G  442 ASP cc_start: 0.8779 (m-30) cc_final: 0.8098 (m-30)
  outliers start: 3
  outliers final: 1
  residues processed: 128
  average time/residue: 0.1876
  time to fit residues: 29.8522
Evaluate side-chains
  103 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 102
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 52 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 31 optimal weight:    0.0980
   chunk 25 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 36 optimal weight:    0.4980
   chunk 56 optimal weight:    0.4980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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**
A  13 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.135186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.114599 restraints weight = 6645.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.118624 restraints weight = 3457.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.121404 restraints weight = 2240.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3503
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3503 r_free = 0.3503    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3503 r_free = 0.3503    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3503
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.1437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5157  Z= 0.146
  Angle     :  0.592   7.006   6997  Z= 0.313
  Chirality :  0.044   0.150    754
  Planarity :  0.005   0.063    891
  Dihedral  :  6.192  69.317    752
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  7.26 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 10.62 %
    Favored  : 86.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -3.22 (0.29), residues: 634
  helix: -4.30 (0.47), residues: 15
  sheet: -1.47 (0.30), residues: 257
  loop : -2.62 (0.27), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP G 436 
 HIS   0.002   0.001   HIS B  91 
 PHE   0.015   0.001   PHE L  46 
 TYR   0.016   0.001   TYR B  94 
 ARG   0.005   0.000   ARG G 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00583 (    1)
  link_NAG-ASN         : angle       4.41923 (    3)
  link_BETA1-4         : bond        0.01038 (    1)
  link_BETA1-4         : angle       1.23528 (    3)
  hydrogen bonds       : bond        0.03764 (  144)
  hydrogen bonds       : angle       6.98286 (  357)
  SS BOND              : bond        0.00283 (    8)
  SS BOND              : angle       1.04257 (   16)
  covalent geometry    : bond        0.00329 ( 5147)
  covalent geometry    : angle       0.58296 ( 6975)

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

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

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 113
  time to evaluate  : 0.562 
Fit side-chains
   revert: symmetry clash
REVERT: L   18 GLU cc_start: 0.7590 (pp20) cc_final: 0.7356 (pp20)
REVERT: L   32 MET cc_start: 0.8600 (tpp) cc_final: 0.8082 (tpp)
REVERT: L   66 SER cc_start: 0.8667 (p) cc_final: 0.8059 (m)
REVERT: L   90 TRP cc_start: 0.8338 (t60) cc_final: 0.7664 (t60)
REVERT: H   19 LYS cc_start: 0.8484 (tttt) cc_final: 0.8145 (tttm)
REVERT: H  105 ASP cc_start: 0.8870 (p0) cc_final: 0.8542 (p0)
REVERT: B   42 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7868 (mt0)
REVERT: A    3 LYS cc_start: 0.8552 (pptt) cc_final: 0.8281 (pttp)
REVERT: A   19 LYS cc_start: 0.8539 (tttt) cc_final: 0.8102 (tttp)
  outliers start: 16
  outliers final: 11
  residues processed: 120
  average time/residue: 0.2753
  time to fit residues: 40.6786
Evaluate side-chains
  112 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 2.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   55 SER
Chi-restraints excluded: chain L residue   81 ASP
Chi-restraints excluded: chain L residue   99 THR
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain G residue  375 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 50 optimal weight:    0.5980
   chunk 4 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0970
   chunk 2 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 31 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  50 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.127719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.107192 restraints weight = 6785.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.110808 restraints weight = 3685.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.113259 restraints weight = 2448.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3482
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3482 r_free = 0.3482    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3482 r_free = 0.3482    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3482
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.1969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5157  Z= 0.147
  Angle     :  0.569   7.857   6997  Z= 0.298
  Chirality :  0.044   0.146    754
  Planarity :  0.005   0.058    891
  Dihedral  :  5.793  60.759    752
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.57 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 12.27 %
    Favored  : 82.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -2.59 (0.30), residues: 634
  helix: -3.82 (0.65), residues: 15
  sheet: -0.92 (0.32), residues: 245
  loop : -2.27 (0.29), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  33 
 HIS   0.002   0.001   HIS L  88 
 PHE   0.010   0.001   PHE L  46 
 TYR   0.015   0.002   TYR B  94 
 ARG   0.005   0.000   ARG G 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00310 (    1)
  link_NAG-ASN         : angle       4.05443 (    3)
  link_BETA1-4         : bond        0.00652 (    1)
  link_BETA1-4         : angle       0.61038 (    3)
  hydrogen bonds       : bond        0.03400 (  144)
  hydrogen bonds       : angle       6.25891 (  357)
  SS BOND              : bond        0.00254 (    8)
  SS BOND              : angle       0.99460 (   16)
  covalent geometry    : bond        0.00340 ( 5147)
  covalent geometry    : angle       0.56162 ( 6975)

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

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

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 108
  time to evaluate  : 0.599 
Fit side-chains
REVERT: L   18 GLU cc_start: 0.7604 (pp20) cc_final: 0.7361 (pp20)
REVERT: L   32 MET cc_start: 0.8577 (tpp) cc_final: 0.8059 (tpp)
REVERT: L   66 SER cc_start: 0.8761 (p) cc_final: 0.8147 (m)
REVERT: L   90 TRP cc_start: 0.8370 (t60) cc_final: 0.7633 (t60)
REVERT: H   19 LYS cc_start: 0.8453 (tttt) cc_final: 0.8084 (tttm)
REVERT: H  105 ASP cc_start: 0.8826 (p0) cc_final: 0.8571 (p0)
REVERT: A    3 LYS cc_start: 0.8496 (pptt) cc_final: 0.8178 (pttp)
REVERT: A   19 LYS cc_start: 0.8658 (tttt) cc_final: 0.8246 (ttmm)
REVERT: G  369 TYR cc_start: 0.8608 (t80) cc_final: 0.8390 (t80)
REVERT: G  468 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7903 (mt)
REVERT: G  503 VAL cc_start: 0.9217 (OUTLIER) cc_final: 0.8745 (t)
  outliers start: 29
  outliers final: 22
  residues processed: 123
  average time/residue: 0.3513
  time to fit residues: 53.2210
Evaluate side-chains
  127 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   55 SER
Chi-restraints excluded: chain L residue   81 ASP
Chi-restraints excluded: chain L residue   99 THR
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   76 MET
Chi-restraints excluded: chain H residue   83 LEU
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain A residue    2 VAL
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   69 ARG
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain G residue  341 VAL
Chi-restraints excluded: chain G residue  353 TRP
Chi-restraints excluded: chain G residue  361 CYS
Chi-restraints excluded: chain G residue  375 SER
Chi-restraints excluded: chain G residue  442 ASP
Chi-restraints excluded: chain G residue  468 ILE
Chi-restraints excluded: chain G residue  503 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 53 optimal weight:    0.6980
   chunk 48 optimal weight:    0.2980
   chunk 1 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  55 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.147791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.127999 restraints weight = 6715.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.131738 restraints weight = 3790.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.134216 restraints weight = 2572.721|
|-----------------------------------------------------------------------------|
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3464
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3464 r_free = 0.3464    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3464 r_free = 0.3464    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3464
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.2229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5157  Z= 0.180
  Angle     :  0.584   7.024   6997  Z= 0.306
  Chirality :  0.045   0.151    754
  Planarity :  0.004   0.059    891
  Dihedral  :  5.860  51.586    752
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.68 %
    Favored  : 91.32 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 15.20 %
    Favored  : 79.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -2.31 (0.31), residues: 634
  helix: -3.30 (0.86), residues: 15
  sheet: -0.69 (0.31), residues: 255
  loop : -2.15 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A  33 
 HIS   0.003   0.001   HIS A  58 
 PHE   0.009   0.001   PHE A  70 
 TYR   0.027   0.002   TYR H  32 
 ARG   0.007   0.001   ARG H  98 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00169 (    1)
  link_NAG-ASN         : angle       3.75929 (    3)
  link_BETA1-4         : bond        0.00695 (    1)
  link_BETA1-4         : angle       0.66836 (    3)
  hydrogen bonds       : bond        0.03263 (  144)
  hydrogen bonds       : angle       5.97921 (  357)
  SS BOND              : bond        0.00282 (    8)
  SS BOND              : angle       1.05505 (   16)
  covalent geometry    : bond        0.00421 ( 5147)
  covalent geometry    : angle       0.57730 ( 6975)

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

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

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 107
  time to evaluate  : 0.514 
Fit side-chains
REVERT: L   18 GLU cc_start: 0.7727 (pp20) cc_final: 0.7483 (pp20)
REVERT: L   32 MET cc_start: 0.8633 (tpp) cc_final: 0.8089 (tpp)
REVERT: L   66 SER cc_start: 0.8777 (p) cc_final: 0.8225 (m)
REVERT: H   19 LYS cc_start: 0.8522 (tttt) cc_final: 0.8064 (tttm)
REVERT: H   91 THR cc_start: 0.9170 (m) cc_final: 0.8957 (t)
REVERT: B    4 MET cc_start: 0.8081 (mmm) cc_final: 0.7347 (mmm)
REVERT: A    3 LYS cc_start: 0.8451 (pptt) cc_final: 0.8217 (pttp)
REVERT: A   19 LYS cc_start: 0.8661 (tttt) cc_final: 0.8177 (tttp)
REVERT: A   25 SER cc_start: 0.8168 (m) cc_final: 0.7831 (p)
REVERT: G  369 TYR cc_start: 0.8718 (t80) cc_final: 0.8471 (t80)
REVERT: G  498 GLN cc_start: 0.8743 (mt0) cc_final: 0.8536 (mt0)
REVERT: G  503 VAL cc_start: 0.9316 (OUTLIER) cc_final: 0.8968 (t)
  outliers start: 31
  outliers final: 24
  residues processed: 122
  average time/residue: 0.1780
  time to fit residues: 27.3821
Evaluate side-chains
  129 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 104
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   41 THR
Chi-restraints excluded: chain L residue   55 SER
Chi-restraints excluded: chain L residue   81 ASP
Chi-restraints excluded: chain L residue   99 THR
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   76 MET
Chi-restraints excluded: chain H residue  121 SER
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain A residue    2 VAL
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   69 ARG
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain G residue  341 VAL
Chi-restraints excluded: chain G residue  353 TRP
Chi-restraints excluded: chain G residue  361 CYS
Chi-restraints excluded: chain G residue  375 SER
Chi-restraints excluded: chain G residue  442 ASP
Chi-restraints excluded: chain G residue  503 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 50 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 58 optimal weight:    0.0040
   chunk 46 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 42 optimal weight:    0.2980
   chunk 14 optimal weight:    0.5980
   chunk 11 optimal weight:    0.8980
   chunk 49 optimal weight:    0.5980
   overall best weight:    0.4192

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

Flipped N/Q/H residues before XYZ refinement:
L  88 HIS
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  55 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.143532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.124213 restraints weight = 6642.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.127852 restraints weight = 3780.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.130362 restraints weight = 2595.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3502
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3502 r_free = 0.3502    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3502 r_free = 0.3502    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3502
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.2445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5157  Z= 0.126
  Angle     :  0.554   6.213   6997  Z= 0.292
  Chirality :  0.044   0.147    754
  Planarity :  0.005   0.057    891
  Dihedral  :  5.658  45.988    752
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  5.49 %
    Allowed  : 16.48 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -2.09 (0.32), residues: 634
  helix: -2.76 (1.09), residues: 15
  sheet: -0.59 (0.31), residues: 257
  loop : -1.98 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A  33 
 HIS   0.004   0.001   HIS L  88 
 PHE   0.008   0.001   PHE A  70 
 TYR   0.015   0.001   TYR H  32 
 ARG   0.006   0.000   ARG G 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00491 (    1)
  link_NAG-ASN         : angle       3.37323 (    3)
  link_BETA1-4         : bond        0.00541 (    1)
  link_BETA1-4         : angle       0.70226 (    3)
  hydrogen bonds       : bond        0.03033 (  144)
  hydrogen bonds       : angle       5.71506 (  357)
  SS BOND              : bond        0.00191 (    8)
  SS BOND              : angle       0.93139 (   16)
  covalent geometry    : bond        0.00291 ( 5147)
  covalent geometry    : angle       0.54836 ( 6975)

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

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

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 109
  time to evaluate  : 0.545 
Fit side-chains
REVERT: L   18 GLU cc_start: 0.7810 (pp20) cc_final: 0.7503 (pp20)
REVERT: L   32 MET cc_start: 0.8647 (tpp) cc_final: 0.8098 (tpp)
REVERT: L   66 SER cc_start: 0.8752 (p) cc_final: 0.8239 (m)
REVERT: L   90 TRP cc_start: 0.8456 (t60) cc_final: 0.7942 (t60)
REVERT: H   19 LYS cc_start: 0.8559 (tttt) cc_final: 0.8090 (tttm)
REVERT: B    4 MET cc_start: 0.7987 (mmm) cc_final: 0.7220 (mmm)
REVERT: A    3 LYS cc_start: 0.8366 (pptt) cc_final: 0.8099 (pttp)
REVERT: A   19 LYS cc_start: 0.8654 (tttt) cc_final: 0.8115 (tttp)
REVERT: A   25 SER cc_start: 0.8065 (m) cc_final: 0.7707 (p)
REVERT: G  369 TYR cc_start: 0.8766 (t80) cc_final: 0.8514 (t80)
REVERT: G  468 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7894 (mt)
REVERT: G  498 GLN cc_start: 0.8755 (mt0) cc_final: 0.8549 (mt0)
REVERT: G  503 VAL cc_start: 0.9165 (OUTLIER) cc_final: 0.8791 (t)
REVERT: G  505 TYR cc_start: 0.9319 (OUTLIER) cc_final: 0.9031 (m-10)
  outliers start: 30
  outliers final: 20
  residues processed: 126
  average time/residue: 0.1805
  time to fit residues: 28.8607
Evaluate side-chains
  126 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 103
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   55 SER
Chi-restraints excluded: chain L residue   81 ASP
Chi-restraints excluded: chain L residue   99 THR
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue  121 SER
Chi-restraints excluded: chain B residue   55 HIS
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain A residue    2 VAL
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   69 ARG
Chi-restraints excluded: chain G residue  341 VAL
Chi-restraints excluded: chain G residue  353 TRP
Chi-restraints excluded: chain G residue  361 CYS
Chi-restraints excluded: chain G residue  375 SER
Chi-restraints excluded: chain G residue  442 ASP
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 G residue  511 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 25 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 37 optimal weight:    0.3980
   chunk 29 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  55 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.121874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.102090 restraints weight = 6886.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.105370 restraints weight = 4047.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.107725 restraints weight = 2797.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3087
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3087 r_free = 0.3087    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3087 r_free = 0.3087    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3087
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.2566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   5157  Z= 0.191
  Angle     :  0.594   6.776   6997  Z= 0.311
  Chirality :  0.045   0.152    754
  Planarity :  0.005   0.059    891
  Dihedral  :  5.803  43.556    752
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.36 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 17.58 %
    Favored  : 76.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -2.09 (0.32), residues: 634
  helix: -2.61 (1.15), residues: 15
  sheet: -0.58 (0.32), residues: 259
  loop : -2.00 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A  33 
 HIS   0.011   0.002   HIS B  55 
 PHE   0.009   0.001   PHE A  70 
 TYR   0.031   0.002   TYR H  32 
 ARG   0.007   0.001   ARG H  98 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00163 (    1)
  link_NAG-ASN         : angle       3.51471 (    3)
  link_BETA1-4         : bond        0.00451 (    1)
  link_BETA1-4         : angle       0.81762 (    3)
  hydrogen bonds       : bond        0.03217 (  144)
  hydrogen bonds       : angle       5.73237 (  357)
  SS BOND              : bond        0.00261 (    8)
  SS BOND              : angle       1.04353 (   16)
  covalent geometry    : bond        0.00453 ( 5147)
  covalent geometry    : angle       0.58789 ( 6975)

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

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

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 106
  time to evaluate  : 0.569 
Fit side-chains
   revert: symmetry clash
REVERT: L   18 GLU cc_start: 0.7598 (pp20) cc_final: 0.7388 (pp20)
REVERT: L   32 MET cc_start: 0.8572 (tpp) cc_final: 0.8036 (tpp)
REVERT: L   66 SER cc_start: 0.8799 (p) cc_final: 0.8232 (m)
REVERT: L   90 TRP cc_start: 0.8557 (t60) cc_final: 0.7848 (t60)
REVERT: H   19 LYS cc_start: 0.8428 (tttt) cc_final: 0.8097 (tttm)
REVERT: H   28 SER cc_start: 0.8870 (t) cc_final: 0.8573 (p)
REVERT: H   91 THR cc_start: 0.9197 (m) cc_final: 0.8957 (t)
REVERT: H  105 ASP cc_start: 0.8946 (p0) cc_final: 0.8712 (p0)
REVERT: B    4 MET cc_start: 0.8117 (mmm) cc_final: 0.7379 (mmm)
REVERT: A    3 LYS cc_start: 0.8498 (pptt) cc_final: 0.8280 (pttp)
REVERT: A   19 LYS cc_start: 0.8651 (tttt) cc_final: 0.8203 (tttp)
REVERT: A   25 SER cc_start: 0.8158 (m) cc_final: 0.7894 (p)
REVERT: G  369 TYR cc_start: 0.8583 (t80) cc_final: 0.8357 (t80)
REVERT: G  503 VAL cc_start: 0.9297 (OUTLIER) cc_final: 0.8910 (t)
  outliers start: 31
  outliers final: 26
  residues processed: 122
  average time/residue: 0.1944
  time to fit residues: 30.2148
Evaluate side-chains
  132 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 105
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   41 THR
Chi-restraints excluded: chain L residue   55 SER
Chi-restraints excluded: chain L residue   81 ASP
Chi-restraints excluded: chain L residue   99 THR
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   76 MET
Chi-restraints excluded: chain H residue  118 THR
Chi-restraints excluded: chain H residue  121 SER
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain B residue   55 HIS
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain A residue    2 VAL
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   69 ARG
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain G residue  341 VAL
Chi-restraints excluded: chain G residue  353 TRP
Chi-restraints excluded: chain G residue  361 CYS
Chi-restraints excluded: chain G residue  375 SER
Chi-restraints excluded: chain G residue  503 VAL
Chi-restraints excluded: chain G residue  511 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0970
   chunk 12 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9990
   chunk 22 optimal weight:    0.5980
   chunk 10 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  55 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.149530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.130649 restraints weight = 6547.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.134311 restraints weight = 3683.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.136806 restraints weight = 2475.752|
|-----------------------------------------------------------------------------|
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3115
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3115 r_free = 0.3115    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3115 r_free = 0.3115    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3115
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.2646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5157  Z= 0.143
  Angle     :  0.568   6.564   6997  Z= 0.296
  Chirality :  0.044   0.152    754
  Planarity :  0.004   0.057    891
  Dihedral  :  5.585  42.940    752
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  6.04 %
    Allowed  : 18.32 %
    Favored  : 75.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -2.00 (0.32), residues: 634
  helix: -2.56 (1.18), residues: 15
  sheet: -0.51 (0.32), residues: 259
  loop : -1.95 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A  33 
 HIS   0.010   0.002   HIS B  55 
 PHE   0.008   0.001   PHE A  70 
 TYR   0.031   0.002   TYR G 473 
 ARG   0.007   0.000   ARG G 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00371 (    1)
  link_NAG-ASN         : angle       3.37394 (    3)
  link_BETA1-4         : bond        0.00627 (    1)
  link_BETA1-4         : angle       0.75366 (    3)
  hydrogen bonds       : bond        0.03010 (  144)
  hydrogen bonds       : angle       5.63483 (  357)
  SS BOND              : bond        0.00213 (    8)
  SS BOND              : angle       0.95459 (   16)
  covalent geometry    : bond        0.00336 ( 5147)
  covalent geometry    : angle       0.56201 ( 6975)

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

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

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 105
  time to evaluate  : 0.499 
Fit side-chains
REVERT: L   18 GLU cc_start: 0.7660 (pp20) cc_final: 0.7401 (pp20)
REVERT: L   32 MET cc_start: 0.8602 (tpp) cc_final: 0.8036 (tpp)
REVERT: L   66 SER cc_start: 0.8769 (p) cc_final: 0.8190 (m)
REVERT: L   90 TRP cc_start: 0.8517 (t60) cc_final: 0.7766 (t60)
REVERT: H   28 SER cc_start: 0.8804 (t) cc_final: 0.8533 (p)
REVERT: H   91 THR cc_start: 0.9195 (m) cc_final: 0.8953 (t)
REVERT: H  105 ASP cc_start: 0.8960 (p0) cc_final: 0.8705 (p0)
REVERT: B    4 MET cc_start: 0.8055 (mmm) cc_final: 0.7319 (mmm)
REVERT: A    3 LYS cc_start: 0.8438 (pptt) cc_final: 0.8158 (pttp)
REVERT: A   19 LYS cc_start: 0.8666 (tttt) cc_final: 0.8161 (tttp)
REVERT: A   25 SER cc_start: 0.8122 (m) cc_final: 0.7806 (p)
REVERT: G  503 VAL cc_start: 0.9278 (OUTLIER) cc_final: 0.8853 (t)
  outliers start: 33
  outliers final: 27
  residues processed: 123
  average time/residue: 0.1841
  time to fit residues: 28.5372
Evaluate side-chains
  132 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 104
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   41 THR
Chi-restraints excluded: chain L residue   55 SER
Chi-restraints excluded: chain L residue   81 ASP
Chi-restraints excluded: chain L residue   99 THR
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue  118 THR
Chi-restraints excluded: chain H residue  121 SER
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain B residue   55 HIS
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain A residue    2 VAL
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   69 ARG
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain G residue  341 VAL
Chi-restraints excluded: chain G residue  353 TRP
Chi-restraints excluded: chain G residue  361 CYS
Chi-restraints excluded: chain G residue  375 SER
Chi-restraints excluded: chain G residue  427 ASP
Chi-restraints excluded: chain G residue  503 VAL
Chi-restraints excluded: chain G residue  511 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   chunk 48 optimal weight:    0.1980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  55 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.120932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.101601 restraints weight = 6857.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.104611 restraints weight = 4095.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.106981 restraints weight = 2883.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3481
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3481 r_free = 0.3481    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3481 r_free = 0.3481    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3481
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.2726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5157  Z= 0.187
  Angle     :  0.607   8.844   6997  Z= 0.315
  Chirality :  0.046   0.171    754
  Planarity :  0.005   0.058    891
  Dihedral  :  5.815  42.820    752
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.83 %
    Favored  : 91.17 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 17.77 %
    Favored  : 76.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -2.00 (0.32), residues: 634
  helix: -2.35 (1.16), residues: 15
  sheet: -0.49 (0.32), residues: 259
  loop : -1.97 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A  33 
 HIS   0.006   0.001   HIS B  55 
 PHE   0.008   0.001   PHE A  70 
 TYR   0.028   0.002   TYR G 473 
 ARG   0.006   0.001   ARG G 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00461 (    1)
  link_NAG-ASN         : angle       3.84908 (    3)
  link_BETA1-4         : bond        0.00531 (    1)
  link_BETA1-4         : angle       0.84319 (    3)
  hydrogen bonds       : bond        0.03203 (  144)
  hydrogen bonds       : angle       5.68834 (  357)
  SS BOND              : bond        0.00272 (    8)
  SS BOND              : angle       1.02009 (   16)
  covalent geometry    : bond        0.00441 ( 5147)
  covalent geometry    : angle       0.60032 ( 6975)

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

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

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 102
  time to evaluate  : 0.561 
Fit side-chains
   revert: symmetry clash
REVERT: L   32 MET cc_start: 0.8616 (tpp) cc_final: 0.8042 (tpp)
REVERT: L   66 SER cc_start: 0.8733 (p) cc_final: 0.8153 (m)
REVERT: H   28 SER cc_start: 0.9047 (t) cc_final: 0.8786 (p)
REVERT: H   91 THR cc_start: 0.9212 (m) cc_final: 0.8992 (t)
REVERT: B    4 MET cc_start: 0.8121 (mmm) cc_final: 0.7312 (mmm)
REVERT: A   19 LYS cc_start: 0.8656 (tttt) cc_final: 0.8164 (tttp)
REVERT: A   25 SER cc_start: 0.8150 (m) cc_final: 0.7852 (p)
REVERT: G  503 VAL cc_start: 0.9320 (OUTLIER) cc_final: 0.9010 (t)
  outliers start: 31
  outliers final: 28
  residues processed: 117
  average time/residue: 0.1824
  time to fit residues: 27.0434
Evaluate side-chains
  132 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 103
  time to evaluate  : 0.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   41 THR
Chi-restraints excluded: chain L residue   55 SER
Chi-restraints excluded: chain L residue   81 ASP
Chi-restraints excluded: chain L residue   99 THR
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   76 MET
Chi-restraints excluded: chain H residue  118 THR
Chi-restraints excluded: chain H residue  121 SER
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain B residue   55 HIS
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain A residue    2 VAL
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   35 ASP
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   69 ARG
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain G residue  341 VAL
Chi-restraints excluded: chain G residue  353 TRP
Chi-restraints excluded: chain G residue  361 CYS
Chi-restraints excluded: chain G residue  375 SER
Chi-restraints excluded: chain G residue  503 VAL
Chi-restraints excluded: chain G residue  511 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0020
   chunk 1 optimal weight:    0.0040
   chunk 40 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 35 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.4800

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

Flipped N/Q/H residues before XYZ refinement:
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  55 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.149353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.129336 restraints weight = 6592.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.133382 restraints weight = 3605.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.135947 restraints weight = 2382.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3120
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3120 r_free = 0.3120    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3119 r_free = 0.3119    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3119
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.2781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5157  Z= 0.140
  Angle     :  0.585   8.115   6997  Z= 0.303
  Chirality :  0.044   0.167    754
  Planarity :  0.005   0.057    891
  Dihedral  :  5.626  42.010    752
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.41 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  5.49 %
    Allowed  : 17.95 %
    Favored  : 76.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -1.82 (0.33), residues: 634
  helix: -2.08 (1.23), residues: 15
  sheet: -0.38 (0.32), residues: 257
  loop : -1.85 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A  33 
 HIS   0.006   0.001   HIS B  55 
 PHE   0.007   0.001   PHE B  62 
 TYR   0.023   0.001   TYR H  32 
 ARG   0.006   0.001   ARG G 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00457 (    1)
  link_NAG-ASN         : angle       3.34240 (    3)
  link_BETA1-4         : bond        0.00587 (    1)
  link_BETA1-4         : angle       0.83110 (    3)
  hydrogen bonds       : bond        0.02982 (  144)
  hydrogen bonds       : angle       5.58981 (  357)
  SS BOND              : bond        0.00219 (    8)
  SS BOND              : angle       0.93568 (   16)
  covalent geometry    : bond        0.00328 ( 5147)
  covalent geometry    : angle       0.57947 ( 6975)

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

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

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 108
  time to evaluate  : 0.573 
Fit side-chains
REVERT: L   18 GLU cc_start: 0.7686 (pp20) cc_final: 0.7424 (pp20)
REVERT: L   32 MET cc_start: 0.8601 (tpp) cc_final: 0.8054 (tpp)
REVERT: L   46 PHE cc_start: 0.8366 (OUTLIER) cc_final: 0.7866 (t80)
REVERT: L   66 SER cc_start: 0.8695 (p) cc_final: 0.8129 (m)
REVERT: H   28 SER cc_start: 0.8834 (t) cc_final: 0.8573 (p)
REVERT: H   91 THR cc_start: 0.9199 (m) cc_final: 0.8950 (t)
REVERT: B    4 MET cc_start: 0.8113 (mmm) cc_final: 0.7333 (mmm)
REVERT: A   19 LYS cc_start: 0.8601 (tttt) cc_final: 0.8244 (ttmm)
REVERT: A   25 SER cc_start: 0.8100 (m) cc_final: 0.7794 (p)
REVERT: G  462 LYS cc_start: 0.8922 (ptpp) cc_final: 0.8349 (mmtt)
  outliers start: 30
  outliers final: 28
  residues processed: 121
  average time/residue: 0.1850
  time to fit residues: 28.4661
Evaluate side-chains
  131 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 102
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   41 THR
Chi-restraints excluded: chain L residue   46 PHE
Chi-restraints excluded: chain L residue   55 SER
Chi-restraints excluded: chain L residue   81 ASP
Chi-restraints excluded: chain L residue   99 THR
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   76 MET
Chi-restraints excluded: chain H residue  118 THR
Chi-restraints excluded: chain H residue  121 SER
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain B residue   55 HIS
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain A residue    2 VAL
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   35 ASP
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   69 ARG
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain G residue  341 VAL
Chi-restraints excluded: chain G residue  353 TRP
Chi-restraints excluded: chain G residue  361 CYS
Chi-restraints excluded: chain G residue  375 SER
Chi-restraints excluded: chain G residue  427 ASP
Chi-restraints excluded: chain G residue  511 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 54 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0970
   chunk 51 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  55 HIS
A  50 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.145217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.125541 restraints weight = 6554.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.129380 restraints weight = 3605.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.131956 restraints weight = 2402.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3065
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3065 r_free = 0.3065    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3065 r_free = 0.3065    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3065
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.2839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.069   5157  Z= 0.245
  Angle     :  0.669   8.747   6997  Z= 0.346
  Chirality :  0.047   0.223    754
  Planarity :  0.005   0.060    891
  Dihedral  :  6.131  44.179    752
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.83 %
    Favored  : 91.17 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 18.50 %
    Favored  : 75.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -1.93 (0.32), residues: 634
  helix: -2.04 (1.23), residues: 15
  sheet: -0.44 (0.33), residues: 256
  loop : -1.95 (0.31), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A  33 
 HIS   0.006   0.002   HIS B  55 
 PHE   0.010   0.001   PHE G 429 
 TYR   0.031   0.002   TYR H  32 
 ARG   0.007   0.001   ARG G 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00006 (    1)
  link_NAG-ASN         : angle       5.42493 (    3)
  link_BETA1-4         : bond        0.00532 (    1)
  link_BETA1-4         : angle       1.03313 (    3)
  hydrogen bonds       : bond        0.03384 (  144)
  hydrogen bonds       : angle       5.78351 (  357)
  SS BOND              : bond        0.00320 (    8)
  SS BOND              : angle       1.10268 (   16)
  covalent geometry    : bond        0.00583 ( 5147)
  covalent geometry    : angle       0.65852 ( 6975)

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

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

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1268 Ramachandran restraints generated.
    634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 103
  time to evaluate  : 0.578 
Fit side-chains
   revert: symmetry clash
REVERT: L   32 MET cc_start: 0.8612 (tpp) cc_final: 0.8036 (tpp)
REVERT: L   46 PHE cc_start: 0.8408 (OUTLIER) cc_final: 0.7830 (t80)
REVERT: L   66 SER cc_start: 0.8763 (p) cc_final: 0.8156 (m)
REVERT: H   28 SER cc_start: 0.8862 (t) cc_final: 0.8628 (p)
REVERT: H   91 THR cc_start: 0.9236 (m) cc_final: 0.8990 (t)
REVERT: A   19 LYS cc_start: 0.8593 (tttt) cc_final: 0.8129 (tttp)
REVERT: G  462 LYS cc_start: 0.8926 (ptpp) cc_final: 0.8394 (mmtt)
  outliers start: 31
  outliers final: 25
  residues processed: 120
  average time/residue: 0.1793
  time to fit residues: 27.1949
Evaluate side-chains
  125 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 99
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   46 PHE
Chi-restraints excluded: chain L residue   55 SER
Chi-restraints excluded: chain L residue   57 VAL
Chi-restraints excluded: chain L residue   81 ASP
Chi-restraints excluded: chain L residue   99 THR
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   76 MET
Chi-restraints excluded: chain H residue  118 THR
Chi-restraints excluded: chain H residue  121 SER
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain B residue   55 HIS
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain A residue    2 VAL
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   69 ARG
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain G residue  341 VAL
Chi-restraints excluded: chain G residue  353 TRP
Chi-restraints excluded: chain G residue  361 CYS
Chi-restraints excluded: chain G residue  375 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 56 optimal weight:    0.3980
   chunk 50 optimal weight:    0.9980
   chunk 47 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 35 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 27 optimal weight:    0.5980
   chunk 14 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0970
   chunk 22 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  55 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.148732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.129141 restraints weight = 6598.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.133172 restraints weight = 3570.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.135832 restraints weight = 2343.145|
|-----------------------------------------------------------------------------|
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3481
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3481 r_free = 0.3481    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3481 r_free = 0.3481    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3481
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.2920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5157  Z= 0.143
  Angle     :  0.605   7.696   6997  Z= 0.315
  Chirality :  0.045   0.203    754
  Planarity :  0.005   0.054    891
  Dihedral  :  5.844  43.576    752
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.41 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 19.05 %
    Favored  : 75.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -1.77 (0.33), residues: 634
  helix: -1.94 (1.26), residues: 15
  sheet: -0.40 (0.33), residues: 258
  loop : -1.77 (0.31), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A  33 
 HIS   0.008   0.002   HIS B  55 
 PHE   0.007   0.001   PHE B  10 
 TYR   0.023   0.001   TYR H  32 
 ARG   0.007   0.000   ARG G 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00510 (    1)
  link_NAG-ASN         : angle       4.42250 (    3)
  link_BETA1-4         : bond        0.00650 (    1)
  link_BETA1-4         : angle       1.02117 (    3)
  hydrogen bonds       : bond        0.03019 (  144)
  hydrogen bonds       : angle       5.58646 (  357)
  SS BOND              : bond        0.00205 (    8)
  SS BOND              : angle       0.93313 (   16)
  covalent geometry    : bond        0.00333 ( 5147)
  covalent geometry    : angle       0.59741 ( 6975)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4863.70 seconds
wall clock time: 88 minutes 11.12 seconds (5291.12 seconds total)