Starting phenix.real_space_refine
on Thu Jun  5 14:48:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wrq_32735/06_2025/7wrq_32735_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wrq_32735/06_2025/7wrq_32735.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wrq_32735/06_2025/7wrq_32735.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wrq_32735/06_2025/7wrq_32735.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wrq_32735/06_2025/7wrq_32735_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wrq_32735/06_2025/7wrq_32735_neut.cif"
  }
  resolution = 3.6
  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=  -0.001 sd=   0.032
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      41      5.16       5
     C    3930      2.51       5
     N    1125      2.21       5
     O    1151      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Residue "B ARG   36": not complete - not flipped  Time to flip 8 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 6247
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4384
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 566, 4384
          Classifications: {'peptide': 566}
          Link IDs: {'PTRANS': 32, 'TRANS': 533}
    Chain: "B"
      Number of atoms: 1269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 167, 1269
          Classifications: {'peptide': 167}
          Link IDs: {'PTRANS': 16, 'TRANS': 150}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen planarities: 1
    Chain: "C"
      Number of atoms: 499
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 499
          Classifications: {'peptide': 65}
          Link IDs: {'PTRANS': 4, 'TRANS': 60}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "D"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 4.11, per 1000 atoms: 0.66
  Number of scatterers: 6247
  At special positions: 0
  Unit cell: (63.576, 98.896, 123.62, 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      41     16.00
     O    1151      8.00
     N    1125      7.00
     C    3930      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=18, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  41 " - pdb=" SG  CYS A  47 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  45 " - pdb=" SG  CYS A  60 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 373 " - pdb=" SG  CYS A 397 " distance=1.73
    Simple disulfide: pdb=" SG  CYS A 540 " - pdb=" SG  CYS A 583 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 542 " - pdb=" SG  CYS A 605 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 566 " - pdb=" SG  CYS A 571 " distance=2.09
    Simple disulfide: pdb=" SG  CYS B  13 " - pdb=" SG  CYS B  40 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  16 " - pdb=" SG  CYS B  42 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  24 " - pdb=" SG  CYS B  43 " distance=2.01
    Simple disulfide: pdb=" SG  CYS B  31 " - pdb=" SG  CYS B  46 " distance=2.10
    Simple disulfide: pdb=" SG  CYS B  54 " - pdb=" SG  CYS B  67 " distance=2.19
    Simple disulfide: pdb=" SG  CYS B  61 " - pdb=" SG  CYS B  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 186 " - pdb=" SG  CYS B 213 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 224 " - pdb=" SG  CYS B 235 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 237 " - pdb=" SG  CYS B 258 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C   6 " - pdb=" SG  CYS C  48 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  18 " - pdb=" SG  CYS C  61 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  47 " - pdb=" SG  CYS C  52 " 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 D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
    NAG-ASN
      " NAG A 701 " - " ASN A  64 "
      " NAG A 702 " - " ASN A  96 "
      " NAG A 703 " - " ASN A 515 "
      " NAG A 704 " - " ASN A 580 "
      " NAG D   1 " - " ASN A 368 "
  Time building additional restraints: 1.60
  Conformation dependent library (CDL) restraints added in 869.2 milliseconds
  

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1450

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 9 sheets defined
      8.6% alpha, 3.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.60
  Creating SS restraints...
    Processing helix  chain 'A' and resid 498 through 502
      removed outlier: 3.754A  pdb=" N   LEU A 502 " --> pdb=" O   ASN A 499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 545 through 554
    Processing helix  chain 'B' and resid 17 through 24
    Processing helix  chain 'B' and resid 75 through 82
    Processing helix  chain 'B' and resid 186 through 195
      removed outlier: 3.883A  pdb=" N   ASP B 192 " --> pdb=" O   ARG B 188 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 8 through 19
    Processing helix  chain 'C' and resid 42 through 50
    Processing helix  chain 'C' and resid 53 through 59
      removed outlier: 3.567A  pdb=" N   LEU C  57 " --> pdb=" O   ASP C  53 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 47
      removed outlier: 6.722A  pdb=" N   VAL A  58 " --> pdb=" O   TRP A  80 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   LEU A  79 " --> pdb=" O   ASN A 104 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 200
      removed outlier: 3.523A  pdb=" N   LEU A 199 " --> pdb=" O   GLU A 222 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ASP A 224 " --> pdb=" O   LEU A 199 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   LEU A 223 " --> pdb=" O   LYS A 246 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   TYR A 248 " --> pdb=" O   LEU A 223 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 366 through 367
      removed outlier: 3.666A  pdb=" N   MET A 367 " --> pdb=" O   SER A 390 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 463 through 464
      removed outlier: 7.082A  pdb=" N   LEU A 463 " --> pdb=" O   ASP A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 561 through 563
    Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11
      removed outlier: 6.300A  pdb=" N   VAL B  10 " --> pdb=" O   LEU B 203 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 35 through 36
    Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54
    Processing sheet with id=AA9, first strand: chain 'B' and resid 222 through 223

    50 hydrogen bonds defined for protein.
    132 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: 1.93 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1181
        1.32 -     1.45: 1573
        1.45 -     1.58: 3579
        1.58 -     1.70: 0
        1.70 -     1.83: 44
  Bond restraints: 6377
  Sorted by residual:
  bond pdb=" C   GLU A 567 "
       pdb=" N   GLY A 568 "
    ideal  model  delta    sigma   weight residual
    1.331  1.574 -0.244 1.46e-02 4.69e+03 2.79e+02
  bond pdb=" C   VAL B  30 "
       pdb=" N   CYS B  31 "
    ideal  model  delta    sigma   weight residual
    1.332  1.525 -0.192 1.40e-02 5.10e+03 1.89e+02
  bond pdb=" C   ILE A 565 "
       pdb=" N   CYS A 566 "
    ideal  model  delta    sigma   weight residual
    1.331  1.206  0.125 1.24e-02 6.50e+03 1.01e+02
  bond pdb=" C   LEU C  64 "
       pdb=" N   LYS C  65 "
    ideal  model  delta    sigma   weight residual
    1.329  1.463 -0.134 1.40e-02 5.10e+03 9.10e+01
  bond pdb=" C   GLU A 394 "
       pdb=" N   GLY A 395 "
    ideal  model  delta    sigma   weight residual
    1.333  1.460 -0.127 1.41e-02 5.03e+03 8.09e+01
  ... (remaining 6372 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.68: 8503
        3.68 -     7.35: 113
        7.35 -    11.03: 16
       11.03 -    14.70: 9
       14.70 -    18.38: 4
  Bond angle restraints: 8645
  Sorted by residual:
  angle pdb=" O   ILE A 565 "
        pdb=" C   ILE A 565 "
        pdb=" N   CYS A 566 "
      ideal   model   delta    sigma   weight residual
     122.57  106.94   15.63 1.25e+00 6.40e-01 1.56e+02
  angle pdb=" O   GLU A 394 "
        pdb=" C   GLU A 394 "
        pdb=" N   GLY A 395 "
      ideal   model   delta    sigma   weight residual
     122.85  135.51  -12.66 1.14e+00 7.69e-01 1.23e+02
  angle pdb=" C   ALA B  32 "
        pdb=" N   GLU B  33 "
        pdb=" CA  GLU B  33 "
      ideal   model   delta    sigma   weight residual
     122.68  138.10  -15.42 1.47e+00 4.63e-01 1.10e+02
  angle pdb=" C   SER A  62 "
        pdb=" N   ARG A  63 "
        pdb=" CA  ARG A  63 "
      ideal   model   delta    sigma   weight residual
     121.69  140.07  -18.38 1.85e+00 2.92e-01 9.87e+01
  angle pdb=" O   ALA A 603 "
        pdb=" C   ALA A 603 "
        pdb=" N   PRO A 604 "
      ideal   model   delta    sigma   weight residual
     121.32  109.96   11.36 1.15e+00 7.56e-01 9.75e+01
  ... (remaining 8640 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.98: 3901
       35.98 -    71.97: 88
       71.97 -   107.95: 13
      107.95 -   143.93: 0
      143.93 -   179.91: 1
  Dihedral angle restraints: 4003
    sinusoidal: 1743
      harmonic: 2260
  Sorted by residual:
  dihedral pdb=" CD  ARG B  36 "
           pdb=" NE  ARG B  36 "
           pdb=" CZ  ARG B  36 "
           pdb=" NH1 ARG B  36 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00 -179.91  179.91     1      1.00e+01 1.00e-02 1.92e+02
  dihedral pdb=" CD  ARG A 160 "
           pdb=" NE  ARG A 160 "
           pdb=" CZ  ARG A 160 "
           pdb=" NH1 ARG A 160 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -79.75   79.75     1      1.00e+01 1.00e-02 7.89e+01
  dihedral pdb=" CB  CYS B  24 "
           pdb=" SG  CYS B  24 "
           pdb=" SG  CYS B  43 "
           pdb=" CB  CYS B  43 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  167.98  -74.98     1      1.00e+01 1.00e-02 7.11e+01
  ... (remaining 4000 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.096: 831
       0.096 -    0.193: 116
       0.193 -    0.289: 21
       0.289 -    0.386: 4
       0.386 -    0.482: 3
  Chirality restraints: 975
  Sorted by residual:
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.17   -0.23 2.00e-02 2.50e+03 1.30e+02
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN A 368 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.92   -0.48 2.00e-01 2.50e+01 5.81e+00
  chirality pdb=" CA  LEU A 398 "
            pdb=" N   LEU A 398 "
            pdb=" C   LEU A 398 "
            pdb=" CB  LEU A 398 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.04    0.47 2.00e-01 2.50e+01 5.60e+00
  ... (remaining 972 not shown)

  Planarity restraints: 1142
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   2 "    0.345 2.00e-02 2.50e+03   2.93e-01 1.07e+03
        pdb=" C7  NAG D   2 "   -0.087 2.00e-02 2.50e+03
        pdb=" C8  NAG D   2 "    0.176 2.00e-02 2.50e+03
        pdb=" N2  NAG D   2 "   -0.514 2.00e-02 2.50e+03
        pdb=" O7  NAG D   2 "    0.080 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 702 "   -0.286 2.00e-02 2.50e+03   2.45e-01 7.53e+02
        pdb=" C7  NAG A 702 "    0.068 2.00e-02 2.50e+03
        pdb=" C8  NAG A 702 "   -0.169 2.00e-02 2.50e+03
        pdb=" N2  NAG A 702 "    0.429 2.00e-02 2.50e+03
        pdb=" O7  NAG A 702 "   -0.042 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 704 "    0.212 2.00e-02 2.50e+03   1.76e-01 3.89e+02
        pdb=" C7  NAG A 704 "   -0.058 2.00e-02 2.50e+03
        pdb=" C8  NAG A 704 "    0.151 2.00e-02 2.50e+03
        pdb=" N2  NAG A 704 "   -0.290 2.00e-02 2.50e+03
        pdb=" O7  NAG A 704 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1139 not shown)

  Histogram of nonbonded interaction distances:
        2.36 -     2.87: 2230
        2.87 -     3.37: 4769
        3.37 -     3.88: 8412
        3.88 -     4.39: 9122
        4.39 -     4.90: 16849
  Nonbonded interactions: 41382
  Sorted by model distance:
  nonbonded pdb=" O   SER A 195 "
            pdb=" OG  SER A 195 "
     model   vdw
     2.357 3.040
  nonbonded pdb=" O   GLU B 189 "
            pdb=" OG1 THR B 193 "
     model   vdw
     2.361 3.040
  nonbonded pdb=" O   SER C  34 "
            pdb=" OG  SER C  34 "
     model   vdw
     2.386 3.040
  nonbonded pdb=" N   GLN A  95 "
            pdb=" O   GLN A  95 "
     model   vdw
     2.398 2.496
  nonbonded pdb=" NH1 ARG A 269 "
            pdb=" OH  TYR B 183 "
     model   vdw
     2.417 3.120
  ... (remaining 41377 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:             1.840
  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:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.080
  Process input model:                     17.970
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
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      :  0.012   0.303   6402  Z= 0.696
  Angle     :  1.380  25.271   8702  Z= 0.845
  Chirality :  0.076   0.482    975
  Planarity :  0.024   0.484   1137
  Dihedral  : 15.483 179.913   2499
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 1.04
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  : 19.87 %
    Favored  : 79.62 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  6.65 %
    Favored  : 92.30 %
  Cbeta Deviations :  0.14 %
  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: -5.87 (0.21), residues: 790
  helix: -2.24 (0.61), residues: 60
  sheet: -4.22 (0.40), residues: 100
  loop : -4.45 (0.17), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 179 
 HIS   0.014   0.002   HIS A 389 
 PHE   0.017   0.002   PHE A 262 
 TYR   0.012   0.002   TYR B 183 
 ARG   0.007   0.000   ARG C  56 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.02790 (    5)
  link_NAG-ASN         : angle       5.98642 (   15)
  link_BETA1-4         : bond        0.00146 (    2)
  link_BETA1-4         : angle       2.58030 (    6)
  hydrogen bonds       : bond        0.25345 (   50)
  hydrogen bonds       : angle       9.05070 (  132)
  SS BOND              : bond        0.08369 (   18)
  SS BOND              : angle       6.62618 (   36)
  covalent geometry    : bond        0.01074 ( 6377)
  covalent geometry    : angle       1.29142 ( 8645)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 0.726 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  545 LYS cc_start: 0.9073 (tttp) cc_final: 0.8872 (tptp)
REVERT: B   37 GLU cc_start: 0.9295 (pt0) cc_final: 0.8467 (pm20)
REVERT: B   49 SER cc_start: 0.9460 (t) cc_final: 0.9195 (p)
REVERT: B   68 GLN cc_start: 0.9127 (mt0) cc_final: 0.8816 (mt0)
REVERT: B   72 ASP cc_start: 0.8863 (p0) cc_final: 0.8576 (p0)
REVERT: B  209 HIS cc_start: 0.8327 (m170) cc_final: 0.8090 (m170)
REVERT: B  243 GLN cc_start: 0.8755 (mp10) cc_final: 0.8243 (mp10)
REVERT: B  259 TYR cc_start: 0.8094 (m-80) cc_final: 0.7892 (m-10)
REVERT: C    5 LEU cc_start: 0.8986 (tp) cc_final: 0.8707 (tt)
  outliers start: 7
  outliers final: 3
  residues processed: 89
  average time/residue: 0.2409
  time to fit residues: 27.2401
Evaluate side-chains
  53 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 50
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 CYS
Chi-restraints excluded: chain A residue  566 CYS
Chi-restraints excluded: chain A residue  571 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 59 optimal weight:    7.9990
   chunk 32 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 601 HIS
B 196 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.088419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.062593 restraints weight = 15090.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.064406 restraints weight = 10174.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.065431 restraints weight = 6257.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.1699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   6402  Z= 0.136
  Angle     :  0.712   6.376   8702  Z= 0.354
  Chirality :  0.044   0.156    975
  Planarity :  0.005   0.056   1137
  Dihedral  : 10.251 179.933   1019
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 2.73
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 11.39 %
    Favored  : 88.35 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 10.57 %
    Favored  : 87.16 %
  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: -5.19 (0.23), residues: 790
  helix: -1.63 (0.59), residues: 68
  sheet: -4.03 (0.37), residues: 113
  loop : -3.90 (0.19), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 173 
 HIS   0.014   0.001   HIS A 601 
 PHE   0.012   0.001   PHE A 416 
 TYR   0.016   0.001   TYR A 208 
 ARG   0.010   0.000   ARG C  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00396 (    5)
  link_NAG-ASN         : angle       2.20475 (   15)
  link_BETA1-4         : bond        0.00402 (    2)
  link_BETA1-4         : angle       2.74242 (    6)
  hydrogen bonds       : bond        0.04286 (   50)
  hydrogen bonds       : angle       6.52882 (  132)
  SS BOND              : bond        0.00532 (   18)
  SS BOND              : angle       1.46566 (   36)
  covalent geometry    : bond        0.00338 ( 6377)
  covalent geometry    : angle       0.69806 ( 8645)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 54
  time to evaluate  : 0.729 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  545 LYS cc_start: 0.9117 (tttp) cc_final: 0.8792 (tptp)
REVERT: B   37 GLU cc_start: 0.9268 (pt0) cc_final: 0.8431 (pm20)
REVERT: B   49 SER cc_start: 0.9443 (t) cc_final: 0.9155 (p)
REVERT: B   73 GLU cc_start: 0.8659 (tp30) cc_final: 0.8364 (tm-30)
REVERT: B  209 HIS cc_start: 0.8375 (m170) cc_final: 0.8129 (m170)
REVERT: B  243 GLN cc_start: 0.8821 (mp10) cc_final: 0.8532 (mp10)
REVERT: B  259 TYR cc_start: 0.8365 (m-80) cc_final: 0.8061 (m-10)
  outliers start: 15
  outliers final: 7
  residues processed: 65
  average time/residue: 0.2211
  time to fit residues: 18.8449
Evaluate side-chains
  54 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  566 CYS
Chi-restraints excluded: chain A residue  571 CYS
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain C residue   33 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 10 optimal weight:    5.9990
   chunk 76 optimal weight:    1.9990
   chunk 58 optimal weight:   20.0000
   chunk 64 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0070
   chunk 65 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0040
   chunk 26 optimal weight:    5.9990
   chunk 52 optimal weight:    0.3980
   chunk 68 optimal weight:    1.9990
   chunk 53 optimal weight:    8.9990
   overall best weight:    0.6612

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

Flipped N/Q/H residues before XYZ refinement:
A 252 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.088818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.061850 restraints weight = 15036.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.064365 restraints weight = 8305.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.066011 restraints weight = 5797.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.2114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6402  Z= 0.111
  Angle     :  0.643   9.643   8702  Z= 0.318
  Chirality :  0.042   0.174    975
  Planarity :  0.004   0.049   1137
  Dihedral  :  8.727 179.730   1018
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 2.57
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 11.39 %
    Favored  : 88.48 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 12.69 %
    Favored  : 85.80 %
  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: -4.72 (0.24), residues: 790
  helix: -1.35 (0.59), residues: 69
  sheet: -3.44 (0.49), residues: 72
  loop : -3.67 (0.20), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 173 
 HIS   0.001   0.000   HIS A 392 
 PHE   0.008   0.001   PHE A 416 
 TYR   0.008   0.001   TYR A  49 
 ARG   0.007   0.000   ARG C  37 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00265 (    5)
  link_NAG-ASN         : angle       1.93969 (   15)
  link_BETA1-4         : bond        0.00534 (    2)
  link_BETA1-4         : angle       2.28011 (    6)
  hydrogen bonds       : bond        0.03526 (   50)
  hydrogen bonds       : angle       6.03757 (  132)
  SS BOND              : bond        0.00235 (   18)
  SS BOND              : angle       0.89559 (   36)
  covalent geometry    : bond        0.00282 ( 6377)
  covalent geometry    : angle       0.63482 ( 8645)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.733 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 TYR cc_start: 0.7951 (t80) cc_final: 0.7438 (t80)
REVERT: A  545 LYS cc_start: 0.9125 (tttp) cc_final: 0.8815 (tptp)
REVERT: B   37 GLU cc_start: 0.9227 (pt0) cc_final: 0.8371 (pm20)
REVERT: B   49 SER cc_start: 0.9455 (t) cc_final: 0.9154 (p)
REVERT: B  243 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8447 (mp10)
REVERT: B  259 TYR cc_start: 0.8268 (m-80) cc_final: 0.8039 (m-10)
  outliers start: 10
  outliers final: 4
  residues processed: 60
  average time/residue: 0.2114
  time to fit residues: 17.4011
Evaluate side-chains
  50 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  566 CYS
Chi-restraints excluded: chain B residue  243 GLN
Chi-restraints excluded: chain B residue  250 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 76 optimal weight:    4.9990
   chunk 56 optimal weight:    3.9990
   chunk 14 optimal weight:    5.9990
   chunk 64 optimal weight:    5.9990
   chunk 77 optimal weight:    0.8980
   chunk 63 optimal weight:    0.2980
   chunk 36 optimal weight:    3.9990
   overall best weight:    2.0384

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

Flipped N/Q/H residues before XYZ refinement:
** A 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 601 HIS
B 196 HIS
B 209 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.083994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2774 r_free = 0.2774 target = 0.057351 restraints weight = 15746.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.059656 restraints weight = 9026.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.061178 restraints weight = 6438.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.2610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   6402  Z= 0.219
  Angle     :  0.731   9.126   8702  Z= 0.366
  Chirality :  0.045   0.153    975
  Planarity :  0.005   0.051   1137
  Dihedral  :  8.459 179.331   1017
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 15.32 %
    Favored  : 84.56 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 14.20 %
    Favored  : 83.84 %
  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: -4.54 (0.24), residues: 790
  helix: -0.95 (0.59), residues: 68
  sheet: -3.44 (0.60), residues: 52
  loop : -3.58 (0.20), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 173 
 HIS   0.007   0.001   HIS B 196 
 PHE   0.011   0.001   PHE A 416 
 TYR   0.012   0.001   TYR C  24 
 ARG   0.007   0.000   ARG C  56 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00327 (    5)
  link_NAG-ASN         : angle       2.09018 (   15)
  link_BETA1-4         : bond        0.00196 (    2)
  link_BETA1-4         : angle       2.09789 (    6)
  hydrogen bonds       : bond        0.04706 (   50)
  hydrogen bonds       : angle       6.23663 (  132)
  SS BOND              : bond        0.00335 (   18)
  SS BOND              : angle       1.05709 (   36)
  covalent geometry    : bond        0.00532 ( 6377)
  covalent geometry    : angle       0.72295 ( 8645)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 43
  time to evaluate  : 0.675 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 TYR cc_start: 0.7998 (t80) cc_final: 0.7655 (t80)
REVERT: A  208 TYR cc_start: 0.8468 (t80) cc_final: 0.8227 (t80)
REVERT: A  346 ASP cc_start: 0.8725 (p0) cc_final: 0.8423 (p0)
REVERT: A  545 LYS cc_start: 0.9154 (tttp) cc_final: 0.8834 (tptp)
REVERT: B   37 GLU cc_start: 0.9178 (pt0) cc_final: 0.8312 (pm20)
REVERT: B   49 SER cc_start: 0.9465 (t) cc_final: 0.9170 (p)
REVERT: B  189 GLU cc_start: 0.8761 (tp30) cc_final: 0.8540 (tp30)
REVERT: B  259 TYR cc_start: 0.8275 (m-80) cc_final: 0.8019 (m-10)
  outliers start: 13
  outliers final: 9
  residues processed: 54
  average time/residue: 0.2101
  time to fit residues: 15.0425
Evaluate side-chains
  49 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 40
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  347 HIS
Chi-restraints excluded: chain A residue  376 ASN
Chi-restraints excluded: chain A residue  566 CYS
Chi-restraints excluded: chain A residue  601 HIS
Chi-restraints excluded: chain B residue  209 HIS
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain C residue   29 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0050
   chunk 55 optimal weight:    6.9990
   chunk 15 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 62 optimal weight:    6.9990
   chunk 4 optimal weight:    0.9990
   chunk 76 optimal weight:    3.9990
   chunk 75 optimal weight:    7.9990
   overall best weight:    1.1198

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

Flipped N/Q/H residues before XYZ refinement:
** A 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 601 HIS
B 209 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.085403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.058636 restraints weight = 15437.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.061047 restraints weight = 8715.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.062671 restraints weight = 6149.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.2767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6402  Z= 0.133
  Angle     :  0.643   8.648   8702  Z= 0.325
  Chirality :  0.042   0.152    975
  Planarity :  0.004   0.049   1137
  Dihedral  :  8.184 179.571   1017
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 11.77 %
    Favored  : 88.10 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 14.80 %
    Favored  : 83.08 %
  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: -4.33 (0.25), residues: 790
  helix: -0.62 (0.59), residues: 69
  sheet: -3.54 (0.51), residues: 70
  loop : -3.40 (0.20), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 236 
 HIS   0.017   0.002   HIS A 601 
 PHE   0.010   0.001   PHE A 416 
 TYR   0.006   0.001   TYR B 183 
 ARG   0.004   0.000   ARG C  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00182 (    5)
  link_NAG-ASN         : angle       1.80977 (   15)
  link_BETA1-4         : bond        0.00351 (    2)
  link_BETA1-4         : angle       1.62995 (    6)
  hydrogen bonds       : bond        0.03677 (   50)
  hydrogen bonds       : angle       5.88661 (  132)
  SS BOND              : bond        0.00229 (   18)
  SS BOND              : angle       0.77869 (   36)
  covalent geometry    : bond        0.00334 ( 6377)
  covalent geometry    : angle       0.63713 ( 8645)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 49
  time to evaluate  : 0.681 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 TYR cc_start: 0.7959 (t80) cc_final: 0.7681 (t80)
REVERT: A  545 LYS cc_start: 0.9154 (tttp) cc_final: 0.8845 (tptp)
REVERT: B   37 GLU cc_start: 0.9147 (pt0) cc_final: 0.8242 (pm20)
REVERT: B   49 SER cc_start: 0.9466 (t) cc_final: 0.9156 (p)
REVERT: B  259 TYR cc_start: 0.8294 (m-80) cc_final: 0.8019 (m-10)
REVERT: C   37 ARG cc_start: 0.7058 (mmm-85) cc_final: 0.6834 (mmm-85)
  outliers start: 14
  outliers final: 9
  residues processed: 60
  average time/residue: 0.1894
  time to fit residues: 15.3253
Evaluate side-chains
  52 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  347 HIS
Chi-restraints excluded: chain A residue  376 ASN
Chi-restraints excluded: chain A residue  566 CYS
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue   33 SER
Chi-restraints excluded: chain C residue   41 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 61 optimal weight:    8.9990
   chunk 31 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 62 optimal weight:   10.0000
   chunk 40 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
** A 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 601 HIS
B 196 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.084991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2783 r_free = 0.2783 target = 0.057849 restraints weight = 15445.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.060180 restraints weight = 8834.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.061726 restraints weight = 6274.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.2846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.2941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   6402  Z= 0.171
  Angle     :  0.673   9.395   8702  Z= 0.340
  Chirality :  0.043   0.158    975
  Planarity :  0.005   0.049   1137
  Dihedral  :  8.144 178.554   1017
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 14.56 %
    Favored  : 85.32 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 15.41 %
    Favored  : 81.87 %
  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: -4.24 (0.26), residues: 790
  helix: -0.25 (0.63), residues: 69
  sheet: -3.56 (0.51), residues: 70
  loop : -3.36 (0.21), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 236 
 HIS   0.015   0.001   HIS A 601 
 PHE   0.010   0.001   PHE A 416 
 TYR   0.009   0.001   TYR C  24 
 ARG   0.005   0.000   ARG C  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00179 (    5)
  link_NAG-ASN         : angle       1.77061 (   15)
  link_BETA1-4         : bond        0.00187 (    2)
  link_BETA1-4         : angle       1.46110 (    6)
  hydrogen bonds       : bond        0.04096 (   50)
  hydrogen bonds       : angle       5.78735 (  132)
  SS BOND              : bond        0.00294 (   18)
  SS BOND              : angle       0.98238 (   36)
  covalent geometry    : bond        0.00425 ( 6377)
  covalent geometry    : angle       0.66667 ( 8645)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 43
  time to evaluate  : 0.834 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 TYR cc_start: 0.7983 (t80) cc_final: 0.7738 (t80)
REVERT: B   37 GLU cc_start: 0.9081 (pt0) cc_final: 0.8259 (pm20)
REVERT: B   49 SER cc_start: 0.9515 (t) cc_final: 0.9209 (p)
REVERT: B  259 TYR cc_start: 0.8225 (m-80) cc_final: 0.7968 (m-10)
REVERT: C   37 ARG cc_start: 0.7176 (mmm-85) cc_final: 0.6947 (mmm-85)
  outliers start: 18
  outliers final: 10
  residues processed: 57
  average time/residue: 0.1978
  time to fit residues: 15.5690
Evaluate side-chains
  52 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 42
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  347 HIS
Chi-restraints excluded: chain A residue  376 ASN
Chi-restraints excluded: chain A residue  566 CYS
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue   33 SER
Chi-restraints excluded: chain C residue   41 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 3 optimal weight:    9.9990
   chunk 75 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
** A 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 601 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.085960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.059415 restraints weight = 15483.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.062152 restraints weight = 9802.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.063989 restraints weight = 5896.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.3116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6402  Z= 0.136
  Angle     :  0.634   9.290   8702  Z= 0.319
  Chirality :  0.042   0.151    975
  Planarity :  0.004   0.049   1137
  Dihedral  :  8.011 179.364   1017
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 3.13
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 11.01 %
    Favored  : 88.86 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 16.47 %
    Favored  : 81.42 %
  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: -4.05 (0.26), residues: 790
  helix: -0.05 (0.65), residues: 69
  sheet: -3.72 (0.53), residues: 60
  loop : -3.22 (0.21), residues: 661

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 236 
 HIS   0.002   0.001   HIS B 196 
 PHE   0.009   0.001   PHE A 416 
 TYR   0.006   0.001   TYR B 183 
 ARG   0.003   0.000   ARG C  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00133 (    5)
  link_NAG-ASN         : angle       1.61433 (   15)
  link_BETA1-4         : bond        0.00276 (    2)
  link_BETA1-4         : angle       1.31736 (    6)
  hydrogen bonds       : bond        0.03382 (   50)
  hydrogen bonds       : angle       5.57824 (  132)
  SS BOND              : bond        0.00258 (   18)
  SS BOND              : angle       0.79220 (   36)
  covalent geometry    : bond        0.00342 ( 6377)
  covalent geometry    : angle       0.62918 ( 8645)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 44
  time to evaluate  : 0.693 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 TYR cc_start: 0.8022 (t80) cc_final: 0.7719 (t80)
REVERT: A  576 TYR cc_start: 0.8500 (m-80) cc_final: 0.8243 (m-10)
REVERT: B   37 GLU cc_start: 0.9030 (pt0) cc_final: 0.8419 (pt0)
REVERT: B   49 SER cc_start: 0.9503 (t) cc_final: 0.9178 (p)
REVERT: B  189 GLU cc_start: 0.8808 (tp30) cc_final: 0.8506 (tp30)
REVERT: B  259 TYR cc_start: 0.8304 (m-80) cc_final: 0.8023 (m-10)
REVERT: C   37 ARG cc_start: 0.7261 (mmm-85) cc_final: 0.6987 (mmm-85)
  outliers start: 14
  outliers final: 10
  residues processed: 54
  average time/residue: 0.2049
  time to fit residues: 14.8134
Evaluate side-chains
  51 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 41
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  347 HIS
Chi-restraints excluded: chain A residue  566 CYS
Chi-restraints excluded: chain A residue  601 HIS
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue   33 SER
Chi-restraints excluded: chain C residue   41 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 58 optimal weight:    8.9990
   chunk 31 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   chunk 22 optimal weight:    0.3980
   chunk 21 optimal weight:    0.0770
   chunk 57 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 0 optimal weight:    9.9990
   chunk 15 optimal weight:    0.9980
   chunk 71 optimal weight:   10.0000
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
** A 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 601 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.086671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.059762 restraints weight = 15300.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.062099 restraints weight = 8637.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.063713 restraints weight = 6129.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.3228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6402  Z= 0.108
  Angle     :  0.620   9.128   8702  Z= 0.311
  Chirality :  0.041   0.153    975
  Planarity :  0.004   0.049   1137
  Dihedral  :  7.898 179.704   1017
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 10.89 %
    Favored  : 88.99 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 16.62 %
    Favored  : 81.42 %
  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: -3.94 (0.26), residues: 790
  helix:  0.02 (0.64), residues: 69
  sheet: -3.66 (0.54), residues: 60
  loop : -3.13 (0.21), residues: 661

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP B 236 
 HIS   0.011   0.001   HIS A 601 
 PHE   0.008   0.001   PHE A 416 
 TYR   0.011   0.001   TYR A 208 
 ARG   0.004   0.000   ARG B  66 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00155 (    5)
  link_NAG-ASN         : angle       1.54122 (   15)
  link_BETA1-4         : bond        0.00282 (    2)
  link_BETA1-4         : angle       1.24743 (    6)
  hydrogen bonds       : bond        0.03027 (   50)
  hydrogen bonds       : angle       5.37965 (  132)
  SS BOND              : bond        0.00195 (   18)
  SS BOND              : angle       0.70043 (   36)
  covalent geometry    : bond        0.00275 ( 6377)
  covalent geometry    : angle       0.61574 ( 8645)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 42
  time to evaluate  : 0.682 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 TYR cc_start: 0.7926 (t80) cc_final: 0.7711 (t80)
REVERT: A  576 TYR cc_start: 0.8456 (m-80) cc_final: 0.8168 (m-10)
REVERT: A  578 TYR cc_start: 0.8993 (m-80) cc_final: 0.8413 (m-10)
REVERT: B   37 GLU cc_start: 0.9021 (pt0) cc_final: 0.8433 (pt0)
REVERT: B   49 SER cc_start: 0.9519 (t) cc_final: 0.9189 (p)
REVERT: B  209 HIS cc_start: 0.8570 (m90) cc_final: 0.8274 (m170)
REVERT: B  259 TYR cc_start: 0.8213 (m-80) cc_final: 0.7973 (m-10)
REVERT: C   37 ARG cc_start: 0.7193 (mmm-85) cc_final: 0.6956 (mmm-85)
  outliers start: 13
  outliers final: 10
  residues processed: 51
  average time/residue: 0.1828
  time to fit residues: 12.9772
Evaluate side-chains
  52 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 42
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  347 HIS
Chi-restraints excluded: chain A residue  566 CYS
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue   33 SER
Chi-restraints excluded: chain C residue   41 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 71 optimal weight:   10.0000
   chunk 59 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 72 optimal weight:    6.9990
   chunk 66 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 64 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 601 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.081832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2758 r_free = 0.2758 target = 0.055936 restraints weight = 15881.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.058231 restraints weight = 10343.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.059092 restraints weight = 6397.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8552
moved from start:          0.3331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.049   6402  Z= 0.302
  Angle     :  0.808   9.203   8702  Z= 0.405
  Chirality :  0.047   0.173    975
  Planarity :  0.005   0.050   1137
  Dihedral  :  8.384 178.761   1017
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 16.58 %
    Favored  : 83.29 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 17.22 %
    Favored  : 81.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -4.20 (0.26), residues: 790
  helix: -0.13 (0.64), residues: 69
  sheet: -3.92 (0.50), residues: 72
  loop : -3.28 (0.21), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 532 
 HIS   0.004   0.001   HIS A 323 
 PHE   0.014   0.002   PHE A 416 
 TYR   0.013   0.001   TYR C  24 
 ARG   0.003   0.000   ARG B  66 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00220 (    5)
  link_NAG-ASN         : angle       1.92008 (   15)
  link_BETA1-4         : bond        0.00168 (    2)
  link_BETA1-4         : angle       1.48919 (    6)
  hydrogen bonds       : bond        0.04951 (   50)
  hydrogen bonds       : angle       5.76932 (  132)
  SS BOND              : bond        0.00388 (   18)
  SS BOND              : angle       1.12322 (   36)
  covalent geometry    : bond        0.00727 ( 6377)
  covalent geometry    : angle       0.80252 ( 8645)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.697 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 TYR cc_start: 0.8075 (t80) cc_final: 0.7747 (t80)
REVERT: B   37 GLU cc_start: 0.8972 (pt0) cc_final: 0.8381 (pt0)
REVERT: B   49 SER cc_start: 0.9513 (t) cc_final: 0.9199 (p)
REVERT: B  259 TYR cc_start: 0.8342 (m-80) cc_final: 0.8056 (m-10)
REVERT: C   37 ARG cc_start: 0.7405 (mmm-85) cc_final: 0.7152 (mmm-85)
  outliers start: 11
  outliers final: 9
  residues processed: 50
  average time/residue: 0.2297
  time to fit residues: 15.0237
Evaluate side-chains
  50 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 41
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  347 HIS
Chi-restraints excluded: chain A residue  566 CYS
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue   33 SER
Chi-restraints excluded: chain C residue   41 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 33 optimal weight:    0.3980
   chunk 60 optimal weight:    0.7980
   chunk 6 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 601 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.085853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.059622 restraints weight = 15582.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.062059 restraints weight = 9962.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.063743 restraints weight = 5966.940|
|-----------------------------------------------------------------------------|
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.3420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6402  Z= 0.115
  Angle     :  0.649   9.530   8702  Z= 0.327
  Chirality :  0.041   0.154    975
  Planarity :  0.004   0.046   1137
  Dihedral  :  8.008 179.782   1017
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 3.05
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 10.51 %
    Favored  : 89.37 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 17.22 %
    Favored  : 81.12 %
  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: -3.94 (0.26), residues: 790
  helix:  0.05 (0.69), residues: 63
  sheet: -3.52 (0.56), residues: 59
  loop : -3.12 (0.21), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 179 
 HIS   0.003   0.001   HIS A 601 
 PHE   0.009   0.001   PHE A 485 
 TYR   0.007   0.001   TYR B 183 
 ARG   0.008   0.000   ARG C  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00144 (    5)
  link_NAG-ASN         : angle       1.51706 (   15)
  link_BETA1-4         : bond        0.00285 (    2)
  link_BETA1-4         : angle       1.25962 (    6)
  hydrogen bonds       : bond        0.03122 (   50)
  hydrogen bonds       : angle       5.43689 (  132)
  SS BOND              : bond        0.00148 (   18)
  SS BOND              : angle       0.69813 (   36)
  covalent geometry    : bond        0.00290 ( 6377)
  covalent geometry    : angle       0.64530 ( 8645)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 45
  time to evaluate  : 0.804 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 TYR cc_start: 0.8016 (t80) cc_final: 0.7701 (t80)
REVERT: B   37 GLU cc_start: 0.8969 (pt0) cc_final: 0.8390 (pt0)
REVERT: B   49 SER cc_start: 0.9524 (t) cc_final: 0.9197 (p)
REVERT: B  209 HIS cc_start: 0.8558 (m90) cc_final: 0.8261 (m170)
REVERT: B  259 TYR cc_start: 0.8338 (m-80) cc_final: 0.8029 (m-10)
REVERT: C   37 ARG cc_start: 0.7473 (mmm-85) cc_final: 0.7178 (mmm-85)
  outliers start: 11
  outliers final: 9
  residues processed: 54
  average time/residue: 0.2277
  time to fit residues: 16.1437
Evaluate side-chains
  51 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 42
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  347 HIS
Chi-restraints excluded: chain A residue  566 CYS
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue   33 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0770
   chunk 45 optimal weight:    0.9990
   chunk 57 optimal weight:    7.9990
   chunk 72 optimal weight:    6.9990
   chunk 61 optimal weight:    0.0010
   chunk 70 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 55 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.7948

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

Flipped N/Q/H residues before XYZ refinement:
** A 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 601 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.086031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.059610 restraints weight = 15771.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.062419 restraints weight = 9708.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.064346 restraints weight = 5774.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.3485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6402  Z= 0.116
  Angle     :  0.627   9.438   8702  Z= 0.315
  Chirality :  0.041   0.152    975
  Planarity :  0.004   0.046   1137
  Dihedral  :  7.867 179.857   1017
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 12.53 %
    Favored  : 87.34 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 16.77 %
    Favored  : 81.87 %
  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: -3.85 (0.27), residues: 790
  helix: -0.06 (0.67), residues: 63
  sheet: -3.52 (0.55), residues: 60
  loop : -3.03 (0.22), residues: 667

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 179 
 HIS   0.001   0.000   HIS A 323 
 PHE   0.009   0.001   PHE A 416 
 TYR   0.006   0.001   TYR B 183 
 ARG   0.003   0.000   ARG C  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00137 (    5)
  link_NAG-ASN         : angle       1.48687 (   15)
  link_BETA1-4         : bond        0.00256 (    2)
  link_BETA1-4         : angle       1.26808 (    6)
  hydrogen bonds       : bond        0.03073 (   50)
  hydrogen bonds       : angle       5.64947 (  132)
  SS BOND              : bond        0.00166 (   18)
  SS BOND              : angle       0.66218 (   36)
  covalent geometry    : bond        0.00295 ( 6377)
  covalent geometry    : angle       0.62372 ( 8645)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2187.42 seconds
wall clock time: 38 minutes 31.25 seconds (2311.25 seconds total)