Starting phenix.real_space_refine
on Wed Jul 23 09:42:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ral_24365/07_2025/7ral_24365.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ral_24365/07_2025/7ral_24365.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ral_24365/07_2025/7ral_24365.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ral_24365/07_2025/7ral_24365.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ral_24365/07_2025/7ral_24365.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ral_24365/07_2025/7ral_24365.cif"
  }
  resolution = 3.7
  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=   0.021
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      14      5.16       5
     C    1825      2.51       5
     N     487      2.21       5
     O     521      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: 2847
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "H"
      Number of atoms: 862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 862
          Classifications: {'peptide': 119}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 2, 'TRANS': 116}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 43
          Unresolved non-hydrogen angles: 54
          Unresolved non-hydrogen dihedrals: 32
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "L"
      Number of atoms: 663
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 663
          Classifications: {'peptide': 99}
          Incomplete info: {'truncation_to_alanine': 29}
          Link IDs: {'PTRANS': 6, 'TRANS': 92}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 59
          Unresolved non-hydrogen angles: 74
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 18
    Chain: "B"
      Number of atoms: 1308
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 171, 1308
          Classifications: {'peptide': 171}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 10, 'TRANS': 160}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 61
          Unresolved non-hydrogen angles: 73
          Unresolved non-hydrogen dihedrals: 51
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 34
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 3.60, per 1000 atoms: 1.26
  Number of scatterers: 2847
  At special positions: 0
  Unit cell: (61.95, 77.7, 61.95, 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      14     16.00
     O     521      8.00
     N     487      7.00
     C    1825      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  90 " distance=2.07
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " 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
    NAG-ASN
      " NAG B1301 " - " ASN B 343 "
  Time building additional restraints: 0.69
  Conformation dependent library (CDL) restraints added in 372.7 milliseconds
  

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  702

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 10 sheets defined
      11.8% alpha, 37.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'H' and resid 62 through 65
    Processing helix  chain 'H' and resid 74 through 77
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 365 through 370
      removed outlier: 3.568A  pdb=" N   ASN B 370 " --> pdb=" O   SER B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 389
      removed outlier: 4.723A  pdb=" N   ASN B 388 " --> pdb=" O   THR B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 4.598A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
    Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 6
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11
      removed outlier: 6.734A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 123 " (cutoff:3.500A)
      removed outlier: 5.375A  pdb=" N   THR H  33 " --> pdb=" O   GLY H  99 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   ILE H  34 " --> pdb=" O   ARG H  50 " (cutoff:3.500A)
      removed outlier: 4.581A  pdb=" N   ARG H  50 " --> pdb=" O   ILE H  34 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   TRP H  36 " --> pdb=" O   MET H  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 11
      removed outlier: 6.734A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 123 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   CYS H  96 " --> pdb=" O   TRP H 116 " (cutoff:3.500A)
      removed outlier: 4.623A  pdb=" N   TRP H 116 " --> pdb=" O   CYS H  96 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   ARG H  98 " --> pdb=" O   ASP H 114 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ASP H 114 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 15 through 20
      removed outlier: 4.481A  pdb=" N   SER H  16 " --> pdb=" O   SER H  85 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 105 through 107
      removed outlier: 3.727A  pdb=" N   ASN B 354 " --> pdb=" O   SER B 399 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 19 through 23
    Processing sheet with id=AA7, first strand: chain 'L' and resid 47 through 50
      removed outlier: 6.564A  pdb=" N   TRP L  37 " --> pdb=" O   LEU L  49 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ASN L 101 " --> pdb=" O   ASP L  94 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 47 through 50
      removed outlier: 6.564A  pdb=" N   TRP L  37 " --> pdb=" O   LEU L  49 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 361 through 362
      removed outlier: 6.462A  pdb=" N   CYS B 361 " --> pdb=" O   CYS B 525 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 452 through 454

    114 hydrogen bonds defined for protein.
    261 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: 0.83

  Time building geometry restraints manager: 0.83 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 569
        1.32 -     1.45: 847
        1.45 -     1.58: 1470
        1.58 -     1.71: 12
        1.71 -     1.84: 18
  Bond restraints: 2916
  Sorted by residual:
  bond pdb=" NE  ARG L  63 "
       pdb=" CZ  ARG L  63 "
    ideal  model  delta    sigma   weight residual
    1.326  1.384 -0.058 1.10e-02 8.26e+03 2.78e+01
  bond pdb=" CB  LEU L 110 "
       pdb=" CG  LEU L 110 "
    ideal  model  delta    sigma   weight residual
    1.530  1.611 -0.081 2.00e-02 2.50e+03 1.64e+01
  bond pdb=" NE  ARG H  50 "
       pdb=" CZ  ARG H  50 "
    ideal  model  delta    sigma   weight residual
    1.326  1.362 -0.036 1.10e-02 8.26e+03 1.08e+01
  bond pdb=" CB  TYR L  38 "
       pdb=" CG  TYR L  38 "
    ideal  model  delta    sigma   weight residual
    1.512  1.441  0.071 2.20e-02 2.07e+03 1.03e+01
  bond pdb=" CG  ASP B 398 "
       pdb=" OD1 ASP B 398 "
    ideal  model  delta    sigma   weight residual
    1.249  1.190  0.059 1.90e-02 2.77e+03 9.54e+00
  ... (remaining 2911 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.80: 3296
        1.80 -     3.59: 547
        3.59 -     5.39: 106
        5.39 -     7.19: 26
        7.19 -     8.98: 2
  Bond angle restraints: 3977
  Sorted by residual:
  angle pdb=" C   GLN B 498 "
        pdb=" N   PRO B 499 "
        pdb=" CA  PRO B 499 "
      ideal   model   delta    sigma   weight residual
     119.56  128.54   -8.98 1.02e+00 9.61e-01 7.76e+01
  angle pdb=" C   ARG L  56 "
        pdb=" N   PRO L  57 "
        pdb=" CA  PRO L  57 "
      ideal   model   delta    sigma   weight residual
     120.03  127.11   -7.08 9.90e-01 1.02e+00 5.12e+01
  angle pdb=" C   ALA B 520 "
        pdb=" N   PRO B 521 "
        pdb=" CA  PRO B 521 "
      ideal   model   delta    sigma   weight residual
     119.56  126.54   -6.98 1.02e+00 9.61e-01 4.68e+01
  angle pdb=" C   GLY L  99 "
        pdb=" N   PRO L 100 "
        pdb=" CA  PRO L 100 "
      ideal   model   delta    sigma   weight residual
     119.76  126.15   -6.39 1.03e+00 9.43e-01 3.85e+01
  angle pdb=" N   SER L  54 "
        pdb=" CA  SER L  54 "
        pdb=" CB  SER L  54 "
      ideal   model   delta    sigma   weight residual
     111.79  104.82    6.97 1.20e+00 6.94e-01 3.37e+01
  ... (remaining 3972 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.78: 1619
       17.78 -    35.57: 57
       35.57 -    53.35: 9
       53.35 -    71.14: 2
       71.14 -    88.92: 3
  Dihedral angle restraints: 1690
    sinusoidal: 582
      harmonic: 1108
  Sorted by residual:
  dihedral pdb=" CB  GLU B 406 "
           pdb=" CG  GLU B 406 "
           pdb=" CD  GLU B 406 "
           pdb=" OE1 GLU B 406 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.92  -88.92     1      3.00e+01 1.11e-03 1.05e+01
  dihedral pdb=" CB  CYS B 391 "
           pdb=" SG  CYS B 391 "
           pdb=" SG  CYS B 525 "
           pdb=" CB  CYS B 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  119.87  -26.87     1      1.00e+01 1.00e-02 1.04e+01
  dihedral pdb=" CA  ARG H  98 "
           pdb=" CB  ARG H  98 "
           pdb=" CG  ARG H  98 "
           pdb=" CD  ARG H  98 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  105.43  -45.43     3      1.50e+01 4.44e-03 8.17e+00
  ... (remaining 1687 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.079: 312
       0.079 -    0.159: 94
       0.159 -    0.238: 20
       0.238 -    0.317: 4
       0.317 -    0.397: 4
  Chirality restraints: 434
  Sorted by residual:
  chirality pdb=" CB  VAL H   2 "
            pdb=" CA  VAL H   2 "
            pdb=" CG1 VAL H   2 "
            pdb=" CG2 VAL H   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -3.03    0.40 2.00e-01 2.50e+01 3.93e+00
  chirality pdb=" C2  NAG B1301 "
            pdb=" C1  NAG B1301 "
            pdb=" C3  NAG B1301 "
            pdb=" N2  NAG B1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.83    0.34 2.00e-01 2.50e+01 2.90e+00
  chirality pdb=" CG  LEU L 110 "
            pdb=" CB  LEU L 110 "
            pdb=" CD1 LEU L 110 "
            pdb=" CD2 LEU L 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.92    0.33 2.00e-01 2.50e+01 2.75e+00
  ... (remaining 431 not shown)

  Planarity restraints: 519
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP L 102 "    0.030 2.00e-02 2.50e+03   1.60e-02 6.39e+00
        pdb=" CG  TRP L 102 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD1 TRP L 102 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 TRP L 102 "   -0.021 2.00e-02 2.50e+03
        pdb=" NE1 TRP L 102 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP L 102 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE3 TRP L 102 "   -0.021 2.00e-02 2.50e+03
        pdb=" CZ2 TRP L 102 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ3 TRP L 102 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP L 102 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR H 104 "    0.028 2.00e-02 2.50e+03   1.47e-02 4.35e+00
        pdb=" CG  TYR H 104 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD1 TYR H 104 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 TYR H 104 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE1 TYR H 104 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 TYR H 104 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR H 104 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR H 104 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP L  37 "   -0.021 2.00e-02 2.50e+03   1.18e-02 3.45e+00
        pdb=" CG  TRP L  37 "    0.006 2.00e-02 2.50e+03
        pdb=" CD1 TRP L  37 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TRP L  37 "    0.014 2.00e-02 2.50e+03
        pdb=" NE1 TRP L  37 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP L  37 "    0.008 2.00e-02 2.50e+03
        pdb=" CE3 TRP L  37 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ2 TRP L  37 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ3 TRP L  37 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP L  37 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 516 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 822
        2.82 -     3.34: 2339
        3.34 -     3.86: 4627
        3.86 -     4.38: 5445
        4.38 -     4.90: 9158
  Nonbonded interactions: 22391
  Sorted by model distance:
  nonbonded pdb=" O   GLY H  27 "
            pdb=" CG1 ILE H  28 "
     model   vdw
     2.298 3.440
  nonbonded pdb=" N   ASP H 114 "
            pdb=" OD1 ASP H 114 "
     model   vdw
     2.477 3.120
  nonbonded pdb=" N   GLY L  30 "
            pdb=" N   ALA L  31 "
     model   vdw
     2.536 2.560
  nonbonded pdb=" OD1 ASN L  28 "
            pdb=" N   ILE L  29 "
     model   vdw
     2.540 3.120
  nonbonded pdb=" OE1 GLU H  46 "
            pdb=" NZ  LYS H  63 "
     model   vdw
     2.565 3.120
  ... (remaining 22386 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             4.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     14.080
  Find NCS groups from input model:        0.030
  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:3.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7322
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      :  0.014   0.081   2922  Z= 0.771
  Angle     :  1.468   8.985   3990  Z= 0.998
  Chirality :  0.086   0.397    434
  Planarity :  0.006   0.037    518
  Dihedral  : 10.313  88.920    973
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 0.56
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  3.22 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  2.76 %
    Favored  : 96.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.43), residues: 373
  helix: -4.68 (0.26), residues: 27
  sheet:  0.49 (0.44), residues: 140
  loop : -0.09 (0.43), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.007   TRP L 102 
 HIS   0.003   0.002   HIS L  36 
 PHE   0.015   0.003   PHE H 113 
 TYR   0.028   0.005   TYR H 104 
 ARG   0.005   0.001   ARG H  98 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.05995 (    1)
  link_NAG-ASN         : angle       2.24467 (    3)
  hydrogen bonds       : bond        0.16198 (  103)
  hydrogen bonds       : angle       9.03477 (  261)
  SS BOND              : bond        0.01804 (    5)
  SS BOND              : angle       2.40214 (   10)
  covalent geometry    : bond        0.01431 ( 2916)
  covalent geometry    : angle       1.46452 ( 3977)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  356 LYS cc_start: 0.8473 (mmmt) cc_final: 0.8236 (mtpt)
  outliers start: 1
  outliers final: 0
  residues processed: 105
  average time/residue: 0.1547
  time to fit residues: 19.1661
Evaluate side-chains
  61 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 31 optimal weight:    0.2980
   chunk 28 optimal weight:    0.9980
   chunk 15 optimal weight:    0.2980
   chunk 9 optimal weight:    0.7980
   chunk 18 optimal weight:    0.6980
   chunk 14 optimal weight:    0.0970
   chunk 29 optimal weight:    0.3980
   chunk 11 optimal weight:    0.5980
   chunk 17 optimal weight:    0.5980
   chunk 21 optimal weight:    0.6980
   chunk 33 optimal weight:    0.1980
   overall best weight:    0.2578

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

Flipped N/Q/H residues before XYZ refinement:
H 103 ASN
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 439 ASN
B 460 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.152387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.143091 restraints weight = 4440.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.145797 restraints weight = 2544.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.147577 restraints weight = 1647.536|
|-----------------------------------------------------------------------------|
r_work (final): 0.3874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7458
moved from start:          0.2706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077   2922  Z= 0.167
  Angle     :  0.658   6.584   3990  Z= 0.345
  Chirality :  0.048   0.138    434
  Planarity :  0.004   0.028    518
  Dihedral  :  4.541  18.059    440
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  2.95 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 14.17 %
    Favored  : 81.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.56 (0.42), residues: 373
  helix: -4.21 (0.62), residues: 27
  sheet:  0.35 (0.41), residues: 147
  loop : -0.27 (0.43), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 436 
 HIS   0.002   0.001   HIS L  36 
 PHE   0.022   0.002   PHE H  29 
 TYR   0.019   0.002   TYR B 369 
 ARG   0.006   0.001   ARG H  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00028 (    1)
  link_NAG-ASN         : angle       2.38384 (    3)
  hydrogen bonds       : bond        0.03497 (  103)
  hydrogen bonds       : angle       6.93057 (  261)
  SS BOND              : bond        0.00436 (    5)
  SS BOND              : angle       1.99350 (   10)
  covalent geometry    : bond        0.00388 ( 2916)
  covalent geometry    : angle       0.64822 ( 3977)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 76
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
  outliers start: 10
  outliers final: 6
  residues processed: 78
  average time/residue: 0.1380
  time to fit residues: 13.0117
Evaluate side-chains
  72 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  121 LEU
Chi-restraints excluded: chain H residue  122 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain B residue  391 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 30 optimal weight:    0.2980
   chunk 11 optimal weight:    0.4980
   chunk 36 optimal weight:    0.3980
   chunk 3 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   chunk 7 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0980
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.3980

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

Flipped N/Q/H residues before XYZ refinement:
H 103 ASN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.128979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.118050 restraints weight = 4518.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.120875 restraints weight = 2647.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.122832 restraints weight = 1729.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.3688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   2922  Z= 0.197
  Angle     :  0.647   6.791   3990  Z= 0.337
  Chirality :  0.047   0.130    434
  Planarity :  0.004   0.035    518
  Dihedral  :  4.608  21.275    440
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.22 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 15.75 %
    Favored  : 79.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.42), residues: 373
  helix: -4.16 (0.68), residues: 27
  sheet:  0.79 (0.44), residues: 130
  loop : -0.26 (0.41), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H 107 
 HIS   0.002   0.001   HIS L  36 
 PHE   0.020   0.002   PHE H  29 
 TYR   0.018   0.002   TYR B 369 
 ARG   0.002   0.000   ARG B 509 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00080 (    1)
  link_NAG-ASN         : angle       1.75516 (    3)
  hydrogen bonds       : bond        0.03337 (  103)
  hydrogen bonds       : angle       6.34378 (  261)
  SS BOND              : bond        0.00746 (    5)
  SS BOND              : angle       1.21431 (   10)
  covalent geometry    : bond        0.00441 ( 2916)
  covalent geometry    : angle       0.64330 ( 3977)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 67
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
REVERT: L   56 ARG cc_start: 0.5596 (mtm-85) cc_final: 0.4872 (ptm-80)
REVERT: B  430 THR cc_start: 0.8800 (m) cc_final: 0.8188 (p)
  outliers start: 12
  outliers final: 8
  residues processed: 72
  average time/residue: 0.1437
  time to fit residues: 12.6173
Evaluate side-chains
  67 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  114 ASP
Chi-restraints excluded: chain H residue  121 LEU
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   75 LEU
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  391 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 34 optimal weight:    0.0980
   chunk 36 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
H 103 ASN
L  40 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.125504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.115692 restraints weight = 4555.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.118251 restraints weight = 2695.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.120043 restraints weight = 1778.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.4468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.067   2922  Z= 0.308
  Angle     :  0.741   8.178   3990  Z= 0.385
  Chirality :  0.049   0.145    434
  Planarity :  0.005   0.042    518
  Dihedral  :  5.390  26.040    440
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.02 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 16.93 %
    Favored  : 77.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.42), residues: 373
  helix: -4.17 (0.67), residues: 27
  sheet:  0.44 (0.42), residues: 131
  loop : -0.54 (0.42), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP H  47 
 HIS   0.001   0.001   HIS L  36 
 PHE   0.023   0.003   PHE H  29 
 TYR   0.024   0.002   TYR B 369 
 ARG   0.004   0.001   ARG B 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00143 (    1)
  link_NAG-ASN         : angle       1.93449 (    3)
  hydrogen bonds       : bond        0.03931 (  103)
  hydrogen bonds       : angle       6.55619 (  261)
  SS BOND              : bond        0.00826 (    5)
  SS BOND              : angle       1.12258 (   10)
  covalent geometry    : bond        0.00684 ( 2916)
  covalent geometry    : angle       0.73811 ( 3977)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
REVERT: L   56 ARG cc_start: 0.5863 (mtm-85) cc_final: 0.5114 (ptm-80)
REVERT: B  430 THR cc_start: 0.8855 (m) cc_final: 0.8284 (p)
REVERT: B  441 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7520 (tt)
  outliers start: 14
  outliers final: 10
  residues processed: 67
  average time/residue: 0.1161
  time to fit residues: 9.8421
Evaluate side-chains
  67 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 56
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  114 ASP
Chi-restraints excluded: chain H residue  121 LEU
Chi-restraints excluded: chain H residue  122 VAL
Chi-restraints excluded: chain L residue   75 LEU
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  391 CYS
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  461 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0980
   chunk 11 optimal weight:    0.3980
   chunk 4 optimal weight:    0.9980
   chunk 7 optimal weight:    0.5980
   chunk 20 optimal weight:    0.0970
   chunk 14 optimal weight:    1.9990
   chunk 35 optimal weight:    0.3980
   chunk 19 optimal weight:    0.3980
   chunk 29 optimal weight:    0.8980
   chunk 10 optimal weight:    0.1980
   overall best weight:    0.2378

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

Flipped N/Q/H residues before XYZ refinement:
L  40 GLN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.130072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.119632 restraints weight = 4479.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.122408 restraints weight = 2594.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.124368 restraints weight = 1687.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.4602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   2922  Z= 0.138
  Angle     :  0.618   6.879   3990  Z= 0.309
  Chirality :  0.045   0.135    434
  Planarity :  0.004   0.040    518
  Dihedral  :  4.589  19.620    440
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  2.68 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 19.69 %
    Favored  : 75.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.70 (0.42), residues: 373
  helix: -4.05 (0.68), residues: 27
  sheet:  0.67 (0.42), residues: 129
  loop : -0.67 (0.41), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 436 
 HIS   0.001   0.001   HIS L  36 
 PHE   0.022   0.002   PHE H  29 
 TYR   0.022   0.001   TYR B 369 
 ARG   0.002   0.000   ARG L  63 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00026 (    1)
  link_NAG-ASN         : angle       1.54068 (    3)
  hydrogen bonds       : bond        0.03078 (  103)
  hydrogen bonds       : angle       6.20238 (  261)
  SS BOND              : bond        0.00578 (    5)
  SS BOND              : angle       0.81134 (   10)
  covalent geometry    : bond        0.00308 ( 2916)
  covalent geometry    : angle       0.61639 ( 3977)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
REVERT: L   49 LEU cc_start: 0.8368 (pp) cc_final: 0.7819 (mt)
REVERT: L   56 ARG cc_start: 0.5828 (mtm-85) cc_final: 0.5125 (ptm160)
REVERT: B  430 THR cc_start: 0.8794 (m) cc_final: 0.8294 (p)
  outliers start: 13
  outliers final: 11
  residues processed: 76
  average time/residue: 0.1270
  time to fit residues: 11.9517
Evaluate side-chains
  77 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   81 MET
Chi-restraints excluded: chain H residue  114 ASP
Chi-restraints excluded: chain H residue  121 LEU
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   75 LEU
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  391 CYS
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  461 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 17 optimal weight:    0.3980
   chunk 28 optimal weight:    0.1980
   chunk 34 optimal weight:    0.0670
   chunk 11 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0670
   chunk 3 optimal weight:    0.0970
   chunk 31 optimal weight:    0.5980
   overall best weight:    0.1654

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

Flipped N/Q/H residues before XYZ refinement:
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.133472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.123122 restraints weight = 4487.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.125924 restraints weight = 2587.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.127901 restraints weight = 1677.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.4833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   2922  Z= 0.110
  Angle     :  0.571   7.598   3990  Z= 0.284
  Chirality :  0.045   0.126    434
  Planarity :  0.004   0.040    518
  Dihedral  :  4.041  17.907    440
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.75 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 22.05 %
    Favored  : 72.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (0.41), residues: 373
  helix: -4.21 (0.60), residues: 27
  sheet:  0.65 (0.42), residues: 131
  loop : -0.77 (0.40), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H 107 
 HIS   0.001   0.001   HIS L  36 
 PHE   0.021   0.002   PHE H  29 
 TYR   0.024   0.001   TYR B 369 
 ARG   0.001   0.000   ARG B 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00141 (    1)
  link_NAG-ASN         : angle       1.11266 (    3)
  hydrogen bonds       : bond        0.02707 (  103)
  hydrogen bonds       : angle       5.95715 (  261)
  SS BOND              : bond        0.00475 (    5)
  SS BOND              : angle       0.74147 (   10)
  covalent geometry    : bond        0.00241 ( 2916)
  covalent geometry    : angle       0.56994 ( 3977)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 71
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
REVERT: L   49 LEU cc_start: 0.8285 (pp) cc_final: 0.7868 (mt)
REVERT: L   56 ARG cc_start: 0.5811 (mtm-85) cc_final: 0.5104 (ptm-80)
REVERT: B  430 THR cc_start: 0.8765 (m) cc_final: 0.8277 (p)
  outliers start: 14
  outliers final: 9
  residues processed: 76
  average time/residue: 0.1252
  time to fit residues: 11.7936
Evaluate side-chains
  73 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  114 ASP
Chi-restraints excluded: chain H residue  121 LEU
Chi-restraints excluded: chain H residue  122 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  391 CYS
Chi-restraints excluded: chain B residue  399 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 6 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 22 optimal weight:    0.2980
   chunk 28 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 14 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
L  40 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.126956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.116030 restraints weight = 4599.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.118848 restraints weight = 2651.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.120777 restraints weight = 1741.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.5175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.068   2922  Z= 0.272
  Angle     :  0.689   7.153   3990  Z= 0.356
  Chirality :  0.048   0.144    434
  Planarity :  0.005   0.047    518
  Dihedral  :  4.947  23.036    440
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.29 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  6.69 %
    Allowed  : 20.47 %
    Favored  : 72.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.06 (0.41), residues: 373
  helix: -4.14 (0.71), residues: 27
  sheet:  0.31 (0.42), residues: 134
  loop : -0.88 (0.41), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP H 116 
 HIS   0.001   0.000   HIS L  36 
 PHE   0.022   0.003   PHE H  29 
 TYR   0.023   0.002   TYR B 369 
 ARG   0.003   0.001   ARG B 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00023 (    1)
  link_NAG-ASN         : angle       1.38331 (    3)
  hydrogen bonds       : bond        0.03536 (  103)
  hydrogen bonds       : angle       6.45472 (  261)
  SS BOND              : bond        0.00690 (    5)
  SS BOND              : angle       1.49943 (   10)
  covalent geometry    : bond        0.00612 ( 2916)
  covalent geometry    : angle       0.68484 ( 3977)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
REVERT: L   56 ARG cc_start: 0.6035 (mtm-85) cc_final: 0.5306 (ptm-80)
REVERT: B  418 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8670 (mt)
REVERT: B  430 THR cc_start: 0.8795 (m) cc_final: 0.8326 (p)
  outliers start: 17
  outliers final: 12
  residues processed: 71
  average time/residue: 0.1246
  time to fit residues: 11.1438
Evaluate side-chains
  77 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  121 LEU
Chi-restraints excluded: chain H residue  122 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  371 SER
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  391 CYS
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  461 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 31 optimal weight:    0.2980
   chunk 23 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 35 optimal weight:    0.5980
   chunk 4 optimal weight:    0.4980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
H  59 ASN
L  40 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.128287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.118258 restraints weight = 4466.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.120934 restraints weight = 2602.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.122751 restraints weight = 1692.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.5335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   2922  Z= 0.233
  Angle     :  0.664   6.988   3990  Z= 0.339
  Chirality :  0.047   0.144    434
  Planarity :  0.005   0.045    518
  Dihedral  :  4.885  23.207    440
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.56 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 21.65 %
    Favored  : 73.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.10 (0.42), residues: 373
  helix: -4.21 (0.66), residues: 27
  sheet:  0.26 (0.42), residues: 136
  loop : -0.90 (0.41), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  47 
 HIS   0.001   0.000   HIS L  36 
 PHE   0.022   0.002   PHE H  29 
 TYR   0.025   0.002   TYR B 369 
 ARG   0.003   0.000   ARG B 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00038 (    1)
  link_NAG-ASN         : angle       1.42380 (    3)
  hydrogen bonds       : bond        0.03377 (  103)
  hydrogen bonds       : angle       6.37924 (  261)
  SS BOND              : bond        0.00646 (    5)
  SS BOND              : angle       1.30531 (   10)
  covalent geometry    : bond        0.00526 ( 2916)
  covalent geometry    : angle       0.66041 ( 3977)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
REVERT: L   49 LEU cc_start: 0.8406 (pp) cc_final: 0.7793 (mt)
REVERT: L   56 ARG cc_start: 0.6039 (mtm-85) cc_final: 0.5287 (ptm-80)
REVERT: B  430 THR cc_start: 0.8789 (m) cc_final: 0.8255 (p)
  outliers start: 13
  outliers final: 12
  residues processed: 72
  average time/residue: 0.1155
  time to fit residues: 10.4468
Evaluate side-chains
  77 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  121 LEU
Chi-restraints excluded: chain H residue  122 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  371 SER
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  391 CYS
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  461 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 5 optimal weight:    0.4980
   chunk 33 optimal weight:    0.9980
   chunk 34 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 15 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.7580

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.124679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.115256 restraints weight = 4532.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.117337 restraints weight = 2818.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.119080 restraints weight = 1965.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.5532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.070   2922  Z= 0.301
  Angle     :  0.719   6.870   3990  Z= 0.372
  Chirality :  0.050   0.154    434
  Planarity :  0.005   0.055    518
  Dihedral  :  5.312  25.970    440
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  5.63 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 22.44 %
    Favored  : 72.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.26 (0.42), residues: 373
  helix: -4.25 (0.68), residues: 27
  sheet:  0.16 (0.43), residues: 136
  loop : -1.02 (0.42), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP H  47 
 HIS   0.001   0.000   HIS L  36 
 PHE   0.026   0.003   PHE H  29 
 TYR   0.025   0.002   TYR B 369 
 ARG   0.002   0.001   ARG B 408 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00090 (    1)
  link_NAG-ASN         : angle       1.65217 (    3)
  hydrogen bonds       : bond        0.03701 (  103)
  hydrogen bonds       : angle       6.63131 (  261)
  SS BOND              : bond        0.00680 (    5)
  SS BOND              : angle       1.32579 (   10)
  covalent geometry    : bond        0.00677 ( 2916)
  covalent geometry    : angle       0.71538 ( 3977)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   56 ARG cc_start: 0.6127 (mtm-85) cc_final: 0.5339 (ptm-80)
REVERT: B  430 THR cc_start: 0.8809 (m) cc_final: 0.8269 (p)
REVERT: B  518 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8328 (pt)
  outliers start: 12
  outliers final: 11
  residues processed: 70
  average time/residue: 0.1117
  time to fit residues: 9.9961
Evaluate side-chains
  78 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  121 LEU
Chi-restraints excluded: chain H residue  122 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  391 CYS
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  518 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 11 optimal weight:    0.5980
   chunk 15 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 36 optimal weight:    0.0770
   chunk 2 optimal weight:    0.7980
   chunk 18 optimal weight:    0.1980
   chunk 32 optimal weight:    0.0270
   chunk 4 optimal weight:    0.6980
   chunk 20 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   overall best weight:    0.3196

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.127538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.117260 restraints weight = 4464.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.119980 restraints weight = 2624.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.121828 restraints weight = 1712.703|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.5527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   2922  Z= 0.154
  Angle     :  0.633   7.803   3990  Z= 0.316
  Chirality :  0.046   0.139    434
  Planarity :  0.005   0.050    518
  Dihedral  :  4.654  21.267    440
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.02 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 23.62 %
    Favored  : 72.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.41), residues: 373
  helix: -4.29 (0.61), residues: 27
  sheet:  0.38 (0.43), residues: 133
  loop : -1.12 (0.41), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H  47 
 HIS   0.001   0.001   HIS L  36 
 PHE   0.024   0.002   PHE H  29 
 TYR   0.023   0.001   TYR B 369 
 ARG   0.001   0.000   ARG B 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00064 (    1)
  link_NAG-ASN         : angle       1.48294 (    3)
  hydrogen bonds       : bond        0.03082 (  103)
  hydrogen bonds       : angle       6.27783 (  261)
  SS BOND              : bond        0.00472 (    5)
  SS BOND              : angle       1.02720 (   10)
  covalent geometry    : bond        0.00348 ( 2916)
  covalent geometry    : angle       0.63071 ( 3977)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
REVERT: L   49 LEU cc_start: 0.8285 (pp) cc_final: 0.7735 (mt)
REVERT: L   56 ARG cc_start: 0.5943 (mtm-85) cc_final: 0.5221 (ptm-80)
REVERT: B  430 THR cc_start: 0.8780 (m) cc_final: 0.8369 (p)
REVERT: B  518 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8277 (pt)
  outliers start: 10
  outliers final: 9
  residues processed: 69
  average time/residue: 0.1251
  time to fit residues: 10.7375
Evaluate side-chains
  73 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  121 LEU
Chi-restraints excluded: chain H residue  122 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  391 CYS
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  518 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 18 optimal weight:    0.2980
   chunk 28 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 13 optimal weight:    0.2980
   chunk 16 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0770
   chunk 4 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.4938

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.127403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.117108 restraints weight = 4449.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.119779 restraints weight = 2636.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.121546 restraints weight = 1745.743|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.5618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   2922  Z= 0.208
  Angle     :  0.648   7.639   3990  Z= 0.328
  Chirality :  0.047   0.141    434
  Planarity :  0.005   0.052    518
  Dihedral  :  4.792  23.237    440
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  5.63 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 22.05 %
    Favored  : 73.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.46 (0.41), residues: 373
  helix: -4.32 (0.62), residues: 27
  sheet:  0.13 (0.42), residues: 137
  loop : -1.26 (0.40), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H  47 
 HIS   0.000   0.000   HIS L  36 
 PHE   0.025   0.002   PHE H  29 
 TYR   0.023   0.002   TYR B 369 
 ARG   0.002   0.000   ARG B 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00015 (    1)
  link_NAG-ASN         : angle       1.56991 (    3)
  hydrogen bonds       : bond        0.03252 (  103)
  hydrogen bonds       : angle       6.35972 (  261)
  SS BOND              : bond        0.00592 (    5)
  SS BOND              : angle       1.10825 (   10)
  covalent geometry    : bond        0.00471 ( 2916)
  covalent geometry    : angle       0.64563 ( 3977)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1488.44 seconds
wall clock time: 26 minutes 27.30 seconds (1587.30 seconds total)