Starting phenix.real_space_refine
on Wed Jul 23 17:24:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sof_25269/07_2025/7sof_25269.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sof_25269/07_2025/7sof_25269.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/7sof_25269/07_2025/7sof_25269.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sof_25269/07_2025/7sof_25269.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sof_25269/07_2025/7sof_25269.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sof_25269/07_2025/7sof_25269.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=   0.045
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      13      5.16       5
     C    2426      2.51       5
     N     611      2.21       5
     O     685      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 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: 3735
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "L"
      Number of atoms: 730
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 730
          Classifications: {'peptide': 105}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PTRANS': 7, 'TRANS': 97}
          Unresolved non-hydrogen bonds: 61
          Unresolved non-hydrogen angles: 76
          Unresolved non-hydrogen dihedrals: 46
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 30
    Chain: "H"
      Number of atoms: 916
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 916
          Classifications: {'peptide': 125}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 7, 'TRANS': 117}
          Unresolved non-hydrogen bonds: 49
          Unresolved non-hydrogen angles: 60
          Unresolved non-hydrogen dihedrals: 38
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 22
    Chain: "A"
      Number of atoms: 1966
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 258, 1966
          Classifications: {'peptide': 258}
          Incomplete info: {'truncation_to_alanine': 45}
          Link IDs: {'PTRANS': 13, 'TRANS': 244}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 135
          Unresolved non-hydrogen angles: 171
          Unresolved non-hydrogen dihedrals: 101
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 77
    Chain: "B"
      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: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 84
          Unusual residues: {'NAG': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
  Time building chain proxies: 5.57, per 1000 atoms: 1.49
  Number of scatterers: 3735
  At special positions: 0
  Unit cell: (73.341, 91.044, 77.556, 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      13     16.00
     O     685      8.00
     N     611      7.00
     C    2426      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  15 " - pdb=" SG  CYS A 136 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 301 " distance=2.02

  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 B   1 " - " NAG B   2 "
      " NAG B   2 " - " BMA B   3 "
    NAG-ASN
      " NAG A1301 " - " ASN A  61 "
      " NAG A1302 " - " ASN A 282 "
      " NAG A1303 " - " ASN A 165 "
      " NAG A1304 " - " ASN A 234 "
      " NAG A1305 " - " ASN A 149 "
      " NAG A1306 " - " ASN A  17 "
      " NAG B   1 " - " ASN A 122 "
  Time building additional restraints: 1.00
  Conformation dependent library (CDL) restraints added in 499.6 milliseconds
  

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  912

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 6 sheets defined
      4.7% alpha, 38.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.42
  Creating SS restraints...
    Processing helix  chain 'L' and resid 78 through 82
      removed outlier: 3.797A  pdb=" N   GLU L  82 " --> pdb=" O   THR L  79 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 65 through 67
      No H-bonds generated for 'chain 'H' and resid 65 through 67'
    Processing helix  chain 'H' and resid 88 through 92
    Processing helix  chain 'A' and resid 294 through 303
    Processing sheet with id=AA1, first strand: chain 'L' and resid 9 through 11
      removed outlier: 6.529A  pdb=" N   VAL L  10 " --> pdb=" O   THR L 104 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   TRP L  34 " --> pdb=" O   VAL L  46 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'L' and resid 18 through 23
    Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12
  WARNING: can't find start of bonding for strands!
    previous: chain 'H' and resid 11 through 12
    current: chain 'H' and resid 48 through 54
  WARNING: can't find start of bonding for strands!
    previous: chain 'H' and resid 59 through 61
    current: chain 'H' and resid 108 through 115
  WARNING: can't find start of bonding for strands!
    previous: chain 'H' and resid 108 through 115
    current: chain 'A' and resid 116 through 121
      removed outlier: 6.601A  pdb=" N   VAL A 126 " --> pdb=" O   TYR A 170 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   TYR A 170 " --> pdb=" O   VAL A 126 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   ILE A 128 " --> pdb=" O   PHE A 168 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   PHE A 168 " --> pdb=" O   ILE A 128 " (cutoff:3.500A)
      removed outlier: 7.314A  pdb=" N   VAL A 130 " --> pdb=" O   CYS A 166 " (cutoff:3.500A)
      removed outlier: 4.645A  pdb=" N   CYS A 166 " --> pdb=" O   VAL A 130 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   SER A 162 " --> pdb=" O   GLN A 134 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   CYS A 136 " --> pdb=" O   TYR A 160 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   TYR A 160 " --> pdb=" O   CYS A 136 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   ASP A 138 " --> pdb=" O   ARG A 158 " (cutoff:3.500A)
      removed outlier: 7.560A  pdb=" N   ARG A 158 " --> pdb=" O   ASP A 138 " (cutoff:3.500A)
      removed outlier: 8.037A  pdb=" N   PHE A 140 " --> pdb=" O   GLU A 156 " (cutoff:3.500A)
      removed outlier: 7.704A  pdb=" N   GLU A 156 " --> pdb=" O   PHE A 140 " (cutoff:3.500A)
      removed outlier: 7.886A  pdb=" N   ASP A 142 " --> pdb=" O   LYS A 154 " (cutoff:3.500A)
      removed outlier: 5.299A  pdb=" N   LYS A 154 " --> pdb=" O   ASP A 142 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   TYR A 144 " --> pdb=" O   TRP A 152 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   TRP A 152 " --> pdb=" O   TYR A 144 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 27 through 31
      removed outlier: 8.484A  pdb=" N   ASN A  61 " --> pdb=" O   TYR A 269 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   TYR A 269 " --> pdb=" O   ASN A  61 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   ALA A 263 " --> pdb=" O   ALA A  67 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   PHE A 201 " --> pdb=" O   ASP A 228 " (cutoff:3.500A)
      removed outlier: 4.755A  pdb=" N   ASP A 228 " --> pdb=" O   PHE A 201 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   ILE A 203 " --> pdb=" O   LEU A 226 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 47 through 55
      removed outlier: 3.711A  pdb=" N   ASP A 287 " --> pdb=" O   LYS A 278 " (cutoff:3.500A)

    116 hydrogen bonds defined for protein.
    288 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: 0.95

  Time building geometry restraints manager: 1.17 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 730
        1.33 -     1.45: 971
        1.45 -     1.57: 2117
        1.57 -     1.70: 0
        1.70 -     1.82: 16
  Bond restraints: 3834
  Sorted by residual:
  bond pdb=" NE  ARG A 246 "
       pdb=" CZ  ARG A 246 "
    ideal  model  delta    sigma   weight residual
    1.326  1.369 -0.043 1.10e-02 8.26e+03 1.50e+01
  bond pdb=" NE  ARG A  78 "
       pdb=" CZ  ARG A  78 "
    ideal  model  delta    sigma   weight residual
    1.326  1.367 -0.041 1.10e-02 8.26e+03 1.41e+01
  bond pdb=" N   ILE L  94 "
       pdb=" CA  ILE L  94 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.19e-02 7.06e+03 8.85e+00
  bond pdb=" C5  NAG A1303 "
       pdb=" O5  NAG A1303 "
    ideal  model  delta    sigma   weight residual
    1.413  1.467 -0.054 2.00e-02 2.50e+03 7.31e+00
  bond pdb=" C5  NAG A1305 "
       pdb=" O5  NAG A1305 "
    ideal  model  delta    sigma   weight residual
    1.413  1.467 -0.054 2.00e-02 2.50e+03 7.17e+00
  ... (remaining 3829 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.49: 4327
        1.49 -     2.99: 734
        2.99 -     4.48: 108
        4.48 -     5.98: 52
        5.98 -     7.47: 27
  Bond angle restraints: 5248
  Sorted by residual:
  angle pdb=" C   GLN H  41 "
        pdb=" N   PRO H  42 "
        pdb=" CA  PRO H  42 "
      ideal   model   delta    sigma   weight residual
     119.66  125.79   -6.13 7.30e-01 1.88e+00 7.05e+01
  angle pdb=" C   ASN A  81 "
        pdb=" N   PRO A  82 "
        pdb=" CA  PRO A  82 "
      ideal   model   delta    sigma   weight residual
     120.03  127.20   -7.17 9.90e-01 1.02e+00 5.24e+01
  angle pdb=" C   GLY H   8 "
        pdb=" N   PRO H   9 "
        pdb=" CA  PRO H   9 "
      ideal   model   delta    sigma   weight residual
     119.76  126.99   -7.23 1.03e+00 9.43e-01 4.93e+01
  angle pdb=" C   ASP A 138 "
        pdb=" N   PRO A 139 "
        pdb=" CA  PRO A 139 "
      ideal   model   delta    sigma   weight residual
     119.76  126.70   -6.94 1.00e+00 1.00e+00 4.82e+01
  angle pdb=" C   ARG L  53 "
        pdb=" N   PRO L  54 "
        pdb=" CA  PRO L  54 "
      ideal   model   delta    sigma   weight residual
     119.85  126.83   -6.98 1.01e+00 9.80e-01 4.78e+01
  ... (remaining 5243 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.32: 2273
       21.32 -    42.64: 44
       42.64 -    63.96: 5
       63.96 -    85.28: 7
       85.28 -   106.60: 4
  Dihedral angle restraints: 2333
    sinusoidal: 916
      harmonic: 1417
  Sorted by residual:
  dihedral pdb=" C   THR L  93 "
           pdb=" N   THR L  93 "
           pdb=" CA  THR L  93 "
           pdb=" CB  THR L  93 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -132.33   10.33     0      2.50e+00 1.60e-01 1.71e+01
  dihedral pdb=" CA  GLY H 105 "
           pdb=" C   GLY H 105 "
           pdb=" N   GLU H 106 "
           pdb=" CA  GLU H 106 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.62   20.38     0      5.00e+00 4.00e-02 1.66e+01
  dihedral pdb=" O4  BMA B   3 "
           pdb=" C4  BMA B   3 "
           pdb=" C5  BMA B   3 "
           pdb=" O5  BMA B   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -71.29 -177.89  106.60     1      3.00e+01 1.11e-03 1.37e+01
  ... (remaining 2330 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 447
       0.070 -    0.139: 136
       0.139 -    0.209: 29
       0.209 -    0.278: 4
       0.278 -    0.348: 10
  Chirality restraints: 626
  Sorted by residual:
  chirality pdb=" C1  BMA B   3 "
            pdb=" O4  NAG B   2 "
            pdb=" C2  BMA B   3 "
            pdb=" O5  BMA B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.52    0.12 2.00e-02 2.50e+03 3.71e+01
  chirality pdb=" C1  NAG B   2 "
            pdb=" O4  NAG B   1 "
            pdb=" C2  NAG B   2 "
            pdb=" O5  NAG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.47    0.07 2.00e-02 2.50e+03 1.13e+01
  chirality pdb=" C5  BMA B   3 "
            pdb=" C4  BMA B   3 "
            pdb=" C6  BMA B   3 "
            pdb=" O5  BMA B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.62    0.35 2.00e-01 2.50e+01 3.03e+00
  ... (remaining 623 not shown)

  Planarity restraints: 659
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR H  96 "    0.034 2.00e-02 2.50e+03   1.80e-02 6.45e+00
        pdb=" CG  TYR H  96 "   -0.016 2.00e-02 2.50e+03
        pdb=" CD1 TYR H  96 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 TYR H  96 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE1 TYR H  96 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 TYR H  96 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR H  96 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR H  96 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY H 105 "    0.012 2.00e-02 2.50e+03   2.40e-02 5.75e+00
        pdb=" C   GLY H 105 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   GLY H 105 "    0.016 2.00e-02 2.50e+03
        pdb=" N   GLU H 106 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A1303 "   -0.026 2.00e-02 2.50e+03   2.12e-02 5.61e+00
        pdb=" C7  NAG A1303 "   -0.003 2.00e-02 2.50e+03
        pdb=" C8  NAG A1303 "   -0.016 2.00e-02 2.50e+03
        pdb=" N2  NAG A1303 "    0.035 2.00e-02 2.50e+03
        pdb=" O7  NAG A1303 "    0.010 2.00e-02 2.50e+03
  ... (remaining 656 not shown)

  Histogram of nonbonded interaction distances:
        2.56 -     3.03: 2165
        3.03 -     3.50: 3156
        3.50 -     3.97: 6049
        3.97 -     4.43: 6775
        4.43 -     4.90: 11258
  Nonbonded interactions: 29403
  Sorted by model distance:
  nonbonded pdb=" ND1 HIS A 146 "
            pdb=" N   LYS A 147 "
     model   vdw
     2.563 3.200
  nonbonded pdb=" O   PRO H  14 "
            pdb=" OG1 THR H  15 "
     model   vdw
     2.593 3.040
  nonbonded pdb=" N   ASN A 148 "
            pdb=" O   ASN A 148 "
     model   vdw
     2.603 2.496
  nonbonded pdb=" N   THR H  10 "
            pdb=" N   LEU H  11 "
     model   vdw
     2.608 2.560
  nonbonded pdb=" OD1 ASP H 113 "
            pdb=" N   VAL H 114 "
     model   vdw
     2.625 3.120
  ... (remaining 29398 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:               0.010
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             7.140
  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:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     16.790
  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:3.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
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      :  0.010   0.062   3848  Z= 0.575
  Angle     :  1.320   7.472   5285  Z= 0.869
  Chirality :  0.080   0.348    626
  Planarity :  0.005   0.024    652
  Dihedral  : 11.425 106.597   1406
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 1.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Cbeta Deviations :  0.22 %
  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:  0.64 (0.38), residues: 474
  helix:  0.56 (1.75), residues: 11
  sheet:  1.23 (0.35), residues: 207
  loop : -0.24 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.004   TRP L  90 
 HIS   0.002   0.001   HIS A 207 
 PHE   0.014   0.003   PHE A 220 
 TYR   0.034   0.005   TYR H  96 
 ARG   0.001   0.000   ARG H  40 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.05510 (    7)
  link_NAG-ASN         : angle       2.65280 (   21)
  link_BETA1-4         : bond        0.05715 (    2)
  link_BETA1-4         : angle       2.83908 (    6)
  hydrogen bonds       : bond        0.16819 (  116)
  hydrogen bonds       : angle       7.97272 (  288)
  SS BOND              : bond        0.00544 (    5)
  SS BOND              : angle       1.93358 (   10)
  covalent geometry    : bond        0.01013 ( 3834)
  covalent geometry    : angle       1.30778 ( 5248)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.391 
Fit side-chains
REVERT: L   36 GLN cc_start: 0.8889 (tt0) cc_final: 0.8628 (tt0)
REVERT: H    3 THR cc_start: 0.7351 (t) cc_final: 0.7149 (m)
REVERT: H   62 SER cc_start: 0.8440 (t) cc_final: 0.8090 (p)
REVERT: H  124 SER cc_start: 0.6718 (p) cc_final: 0.6437 (t)
REVERT: A  154 LYS cc_start: 0.8401 (ttpt) cc_final: 0.8074 (ttpp)
REVERT: A  258 TRP cc_start: 0.7458 (m-90) cc_final: 0.7186 (m-90)
  outliers start: 0
  outliers final: 0
  residues processed: 89
  average time/residue: 0.1781
  time to fit residues: 19.1693
Evaluate side-chains
  63 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 39 optimal weight:    0.0470
   chunk 35 optimal weight:    0.5980
   chunk 19 optimal weight:    0.7980
   chunk 12 optimal weight:    0.8980
   chunk 24 optimal weight:    3.9990
   chunk 36 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   chunk 42 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.5278

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

Flipped N/Q/H residues before XYZ refinement:
L  49 GLN
H  79 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.186913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.155501 restraints weight = 4060.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.156504 restraints weight = 2990.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.158260 restraints weight = 3061.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.2076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3848  Z= 0.161
  Angle     :  0.627   6.341   5285  Z= 0.321
  Chirality :  0.047   0.154    626
  Planarity :  0.005   0.051    652
  Dihedral  :  8.101  60.530    704
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 1.96
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  1.48 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  :  7.35 %
    Favored  : 91.18 %
  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:  0.84 (0.39), residues: 474
  helix:  1.69 (1.55), residues: 11
  sheet:  1.38 (0.38), residues: 191
  loop : -0.07 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H 103 
 HIS   0.002   0.001   HIS A 245 
 PHE   0.015   0.002   PHE A  55 
 TYR   0.026   0.002   TYR L  48 
 ARG   0.004   0.000   ARG A 102 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00265 (    7)
  link_NAG-ASN         : angle       2.03956 (   21)
  link_BETA1-4         : bond        0.00415 (    2)
  link_BETA1-4         : angle       2.63715 (    6)
  hydrogen bonds       : bond        0.03616 (  116)
  hydrogen bonds       : angle       6.19491 (  288)
  SS BOND              : bond        0.00278 (    5)
  SS BOND              : angle       1.62007 (   10)
  covalent geometry    : bond        0.00381 ( 3834)
  covalent geometry    : angle       0.60544 ( 5248)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.423 
Fit side-chains
REVERT: L   53 ARG cc_start: 0.8070 (mtm-85) cc_final: 0.7867 (mtm110)
REVERT: A  108 THR cc_start: 0.8634 (p) cc_final: 0.8214 (t)
REVERT: A  138 ASP cc_start: 0.7993 (t0) cc_final: 0.7761 (t0)
REVERT: A  154 LYS cc_start: 0.8617 (ttpt) cc_final: 0.8280 (ttpp)
REVERT: A  258 TRP cc_start: 0.8194 (m-90) cc_final: 0.7739 (m-90)
  outliers start: 5
  outliers final: 2
  residues processed: 69
  average time/residue: 0.1665
  time to fit residues: 14.0325
Evaluate side-chains
  67 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 65
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   30 THR
Chi-restraints excluded: chain H residue   83 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 45 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
A 121 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.184838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.153120 restraints weight = 4165.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.155900 restraints weight = 3180.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.156678 restraints weight = 3209.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.2902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   3848  Z= 0.238
  Angle     :  0.638   6.134   5285  Z= 0.329
  Chirality :  0.046   0.160    626
  Planarity :  0.005   0.054    652
  Dihedral  :  6.113  38.072    704
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  :  7.06 %
    Favored  : 88.82 %
  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:  0.43 (0.38), residues: 474
  helix:  2.85 (1.62), residues: 11
  sheet:  1.06 (0.37), residues: 191
  loop : -0.39 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP H  49 
 HIS   0.004   0.001   HIS A 245 
 PHE   0.014   0.002   PHE A 238 
 TYR   0.017   0.002   TYR L  48 
 ARG   0.002   0.000   ARG A  78 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00300 (    7)
  link_NAG-ASN         : angle       1.52931 (   21)
  link_BETA1-4         : bond        0.00783 (    2)
  link_BETA1-4         : angle       2.40680 (    6)
  hydrogen bonds       : bond        0.03841 (  116)
  hydrogen bonds       : angle       6.03055 (  288)
  SS BOND              : bond        0.00467 (    5)
  SS BOND              : angle       1.67413 (   10)
  covalent geometry    : bond        0.00565 ( 3834)
  covalent geometry    : angle       0.62379 ( 5248)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.638 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  154 LYS cc_start: 0.8718 (ttpt) cc_final: 0.8348 (ttpp)
  outliers start: 14
  outliers final: 10
  residues processed: 72
  average time/residue: 0.2558
  time to fit residues: 21.8599
Evaluate side-chains
  66 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   30 THR
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain H residue   15 THR
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   83 THR
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  131 CYS
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain A residue  284 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 39 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 45 optimal weight:    6.9990
   chunk 9 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 3 optimal weight:    0.4980
   chunk 30 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9990
   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  88 GLN
A 121 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.161523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.129864 restraints weight = 4296.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.130473 restraints weight = 3542.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.132301 restraints weight = 3653.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.3231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3848  Z= 0.165
  Angle     :  0.580   7.837   5285  Z= 0.295
  Chirality :  0.046   0.160    626
  Planarity :  0.004   0.047    652
  Dihedral  :  5.381  36.937    704
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  :  8.82 %
    Favored  : 87.94 %
  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:  0.27 (0.38), residues: 474
  helix:  3.15 (1.65), residues: 11
  sheet:  0.92 (0.36), residues: 190
  loop : -0.48 (0.37), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H 103 
 HIS   0.002   0.001   HIS A 245 
 PHE   0.012   0.002   PHE A 238 
 TYR   0.017   0.002   TYR L  48 
 ARG   0.012   0.001   ARG A 158 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00271 (    7)
  link_NAG-ASN         : angle       1.58044 (   21)
  link_BETA1-4         : bond        0.00576 (    2)
  link_BETA1-4         : angle       2.21997 (    6)
  hydrogen bonds       : bond        0.03395 (  116)
  hydrogen bonds       : angle       5.77086 (  288)
  SS BOND              : bond        0.00334 (    5)
  SS BOND              : angle       1.38551 (   10)
  covalent geometry    : bond        0.00386 ( 3834)
  covalent geometry    : angle       0.56479 ( 5248)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 56
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 LYS cc_start: 0.8626 (ttpt) cc_final: 0.8326 (ttpp)
REVERT: A  258 TRP cc_start: 0.8008 (m-90) cc_final: 0.7605 (m-90)
  outliers start: 11
  outliers final: 9
  residues processed: 64
  average time/residue: 0.2124
  time to fit residues: 16.1972
Evaluate side-chains
  61 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   27 LEU
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain H residue   15 THR
Chi-restraints excluded: chain H residue   52 LEU
Chi-restraints excluded: chain H residue   83 THR
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  131 CYS
Chi-restraints excluded: chain A residue  210 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 39 optimal weight:    7.9990
   chunk 34 optimal weight:    0.4980
   chunk 25 optimal weight:    5.9990
   chunk 20 optimal weight:    0.4980
   chunk 33 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 125 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.160263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.126645 restraints weight = 4408.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.127442 restraints weight = 3459.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.129141 restraints weight = 3538.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.3521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3848  Z= 0.185
  Angle     :  0.588   8.695   5285  Z= 0.298
  Chirality :  0.045   0.164    626
  Planarity :  0.004   0.046    652
  Dihedral  :  5.359  38.033    704
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  :  8.24 %
    Favored  : 87.94 %
  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:  0.25 (0.38), residues: 474
  helix:  3.23 (1.64), residues: 11
  sheet:  0.78 (0.36), residues: 191
  loop : -0.39 (0.38), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H 115 
 HIS   0.003   0.001   HIS A 245 
 PHE   0.013   0.002   PHE A 238 
 TYR   0.015   0.002   TYR L  48 
 ARG   0.007   0.001   ARG A 158 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00249 (    7)
  link_NAG-ASN         : angle       1.50964 (   21)
  link_BETA1-4         : bond        0.00557 (    2)
  link_BETA1-4         : angle       2.01791 (    6)
  hydrogen bonds       : bond        0.03416 (  116)
  hydrogen bonds       : angle       5.70938 (  288)
  SS BOND              : bond        0.00378 (    5)
  SS BOND              : angle       1.52540 (   10)
  covalent geometry    : bond        0.00440 ( 3834)
  covalent geometry    : angle       0.57422 ( 5248)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 51
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 LYS cc_start: 0.8720 (ttpt) cc_final: 0.8355 (ttpp)
REVERT: A  258 TRP cc_start: 0.8074 (m-90) cc_final: 0.7585 (m-90)
  outliers start: 13
  outliers final: 10
  residues processed: 60
  average time/residue: 0.1965
  time to fit residues: 14.2904
Evaluate side-chains
  61 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 51
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   27 LEU
Chi-restraints excluded: chain L residue   30 THR
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain H residue   15 THR
Chi-restraints excluded: chain H residue   52 LEU
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   83 THR
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  131 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 23 optimal weight:    0.6980
   chunk 4 optimal weight:    0.0870
   chunk 6 optimal weight:    2.9990
   chunk 27 optimal weight:    0.3980
   chunk 33 optimal weight:    0.0030
   chunk 17 optimal weight:    0.9980
   chunk 29 optimal weight:    0.0980
   chunk 11 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   chunk 15 optimal weight:    0.3980
   overall best weight:    0.1968

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.160367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.128803 restraints weight = 4329.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.129694 restraints weight = 3937.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.131176 restraints weight = 3876.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.3637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3848  Z= 0.096
  Angle     :  0.535   7.405   5285  Z= 0.269
  Chirality :  0.045   0.160    626
  Planarity :  0.004   0.041    652
  Dihedral  :  4.924  35.614    704
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 10.00 %
    Favored  : 87.65 %
  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:  0.34 (0.39), residues: 474
  helix:  3.31 (1.66), residues: 11
  sheet:  0.89 (0.36), residues: 195
  loop : -0.40 (0.39), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H 115 
 HIS   0.005   0.001   HIS A 207 
 PHE   0.012   0.001   PHE A  55 
 TYR   0.015   0.001   TYR L  48 
 ARG   0.007   0.001   ARG A 246 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00317 (    7)
  link_NAG-ASN         : angle       1.36685 (   21)
  link_BETA1-4         : bond        0.00600 (    2)
  link_BETA1-4         : angle       2.00009 (    6)
  hydrogen bonds       : bond        0.02900 (  116)
  hydrogen bonds       : angle       5.43462 (  288)
  SS BOND              : bond        0.00203 (    5)
  SS BOND              : angle       1.06935 (   10)
  covalent geometry    : bond        0.00210 ( 3834)
  covalent geometry    : angle       0.52309 ( 5248)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 LYS cc_start: 0.8707 (ttpt) cc_final: 0.8316 (ttpp)
REVERT: A  258 TRP cc_start: 0.8067 (m-90) cc_final: 0.7551 (m-90)
  outliers start: 8
  outliers final: 7
  residues processed: 62
  average time/residue: 0.1930
  time to fit residues: 14.5963
Evaluate side-chains
  60 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain H residue   15 THR
Chi-restraints excluded: chain H residue   24 LEU
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   83 THR
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue  131 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 9 optimal weight:    0.2980
   chunk 41 optimal weight:    0.4980
   chunk 36 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0570
   chunk 13 optimal weight:    0.9990
   chunk 45 optimal weight:    0.3980
   overall best weight:    0.4098

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

Flipped N/Q/H residues before XYZ refinement:
A 125 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.161875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.130050 restraints weight = 4279.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.131278 restraints weight = 3654.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.132585 restraints weight = 3735.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.3764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3848  Z= 0.122
  Angle     :  0.554   8.767   5285  Z= 0.273
  Chirality :  0.045   0.166    626
  Planarity :  0.004   0.043    652
  Dihedral  :  4.870  35.918    704
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 11.18 %
    Favored  : 86.76 %
  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:  0.32 (0.39), residues: 474
  helix:  3.51 (1.69), residues: 11
  sheet:  0.88 (0.36), residues: 195
  loop : -0.42 (0.39), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 115 
 HIS   0.002   0.001   HIS A 207 
 PHE   0.016   0.001   PHE A  55 
 TYR   0.014   0.001   TYR A 265 
 ARG   0.006   0.001   ARG A 246 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00274 (    7)
  link_NAG-ASN         : angle       1.35278 (   21)
  link_BETA1-4         : bond        0.00590 (    2)
  link_BETA1-4         : angle       1.92795 (    6)
  hydrogen bonds       : bond        0.02938 (  116)
  hydrogen bonds       : angle       5.33725 (  288)
  SS BOND              : bond        0.00267 (    5)
  SS BOND              : angle       1.21356 (   10)
  covalent geometry    : bond        0.00284 ( 3834)
  covalent geometry    : angle       0.54261 ( 5248)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 LYS cc_start: 0.8662 (ttpt) cc_final: 0.8305 (ttpp)
  outliers start: 7
  outliers final: 7
  residues processed: 56
  average time/residue: 0.2044
  time to fit residues: 13.8205
Evaluate side-chains
  57 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain H residue   15 THR
Chi-restraints excluded: chain H residue   24 LEU
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   83 THR
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue  131 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0010
   chunk 12 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 11 optimal weight:    0.0870
   overall best weight:    0.5564

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.163276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.131688 restraints weight = 4350.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.132349 restraints weight = 4073.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.134389 restraints weight = 3838.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.3871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3848  Z= 0.144
  Angle     :  0.547   7.333   5285  Z= 0.275
  Chirality :  0.045   0.164    626
  Planarity :  0.004   0.042    652
  Dihedral  :  4.956  36.562    704
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 10.88 %
    Favored  : 86.76 %
  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:  0.31 (0.39), residues: 474
  helix:  3.29 (1.68), residues: 11
  sheet:  0.82 (0.37), residues: 191
  loop : -0.36 (0.39), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 115 
 HIS   0.002   0.001   HIS A 146 
 PHE   0.018   0.002   PHE A  55 
 TYR   0.015   0.001   TYR A 265 
 ARG   0.005   0.001   ARG A 246 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00268 (    7)
  link_NAG-ASN         : angle       1.35444 (   21)
  link_BETA1-4         : bond        0.00505 (    2)
  link_BETA1-4         : angle       1.84982 (    6)
  hydrogen bonds       : bond        0.03032 (  116)
  hydrogen bonds       : angle       5.35370 (  288)
  SS BOND              : bond        0.00299 (    5)
  SS BOND              : angle       1.33995 (   10)
  covalent geometry    : bond        0.00341 ( 3834)
  covalent geometry    : angle       0.53555 ( 5248)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 50
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 LYS cc_start: 0.8708 (ttpt) cc_final: 0.8333 (ttpp)
  outliers start: 8
  outliers final: 8
  residues processed: 56
  average time/residue: 0.2062
  time to fit residues: 13.9498
Evaluate side-chains
  58 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 50
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain H residue   15 THR
Chi-restraints excluded: chain H residue   24 LEU
Chi-restraints excluded: chain H residue   52 LEU
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   83 THR
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue  131 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 25 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 26 optimal weight:    0.5980
   chunk 15 optimal weight:    0.6980
   chunk 34 optimal weight:    0.5980
   chunk 21 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9980
   chunk 41 optimal weight:    0.0870
   chunk 35 optimal weight:    0.9980
   chunk 29 optimal weight:    0.2980
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
A 125 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.163579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.132286 restraints weight = 4266.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.132061 restraints weight = 3875.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.133470 restraints weight = 4371.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.3981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3848  Z= 0.122
  Angle     :  0.551   7.994   5285  Z= 0.272
  Chirality :  0.045   0.162    626
  Planarity :  0.004   0.041    652
  Dihedral  :  4.871  35.903    704
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 11.47 %
    Favored  : 86.18 %
  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 (0.39), residues: 474
  helix:  3.53 (1.73), residues: 11
  sheet:  0.85 (0.37), residues: 191
  loop : -0.37 (0.39), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 115 
 HIS   0.003   0.001   HIS A 207 
 PHE   0.020   0.001   PHE A  55 
 TYR   0.015   0.001   TYR A 265 
 ARG   0.007   0.001   ARG A 246 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00282 (    7)
  link_NAG-ASN         : angle       1.33901 (   21)
  link_BETA1-4         : bond        0.00435 (    2)
  link_BETA1-4         : angle       1.82541 (    6)
  hydrogen bonds       : bond        0.02952 (  116)
  hydrogen bonds       : angle       5.30403 (  288)
  SS BOND              : bond        0.00262 (    5)
  SS BOND              : angle       1.24783 (   10)
  covalent geometry    : bond        0.00286 ( 3834)
  covalent geometry    : angle       0.53970 ( 5248)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 LYS cc_start: 0.8667 (ttpt) cc_final: 0.8318 (ttpp)
  outliers start: 8
  outliers final: 7
  residues processed: 57
  average time/residue: 0.1957
  time to fit residues: 13.5404
Evaluate side-chains
  57 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   27 LEU
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain H residue   15 THR
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   83 THR
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue  131 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 15 optimal weight:    0.4980
   chunk 31 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 1 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.159256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.128437 restraints weight = 4397.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.126552 restraints weight = 4881.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.128773 restraints weight = 4870.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.4118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   3848  Z= 0.200
  Angle     :  0.593   7.858   5285  Z= 0.301
  Chirality :  0.046   0.163    626
  Planarity :  0.004   0.046    652
  Dihedral  :  5.211  38.111    704
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 11.47 %
    Favored  : 85.29 %
  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:  0.07 (0.39), residues: 474
  helix:  3.23 (1.69), residues: 11
  sheet:  0.63 (0.36), residues: 191
  loop : -0.49 (0.39), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 258 
 HIS   0.004   0.001   HIS A 245 
 PHE   0.019   0.002   PHE A  55 
 TYR   0.016   0.002   TYR A 265 
 ARG   0.004   0.001   ARG A 158 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00251 (    7)
  link_NAG-ASN         : angle       1.44523 (   21)
  link_BETA1-4         : bond        0.00503 (    2)
  link_BETA1-4         : angle       1.77826 (    6)
  hydrogen bonds       : bond        0.03327 (  116)
  hydrogen bonds       : angle       5.51488 (  288)
  SS BOND              : bond        0.00381 (    5)
  SS BOND              : angle       1.61711 (   10)
  covalent geometry    : bond        0.00479 ( 3834)
  covalent geometry    : angle       0.58049 ( 5248)

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

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

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  948 Ramachandran restraints generated.
    474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 LYS cc_start: 0.8658 (ttpt) cc_final: 0.8336 (ttpp)
  outliers start: 11
  outliers final: 9
  residues processed: 61
  average time/residue: 0.2075
  time to fit residues: 15.1775
Evaluate side-chains
  61 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   27 LEU
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue   82 GLU
Chi-restraints excluded: chain H residue   15 THR
Chi-restraints excluded: chain H residue   52 LEU
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   83 THR
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue  131 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 43 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 6 optimal weight:    3.9990
   chunk 32 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 37 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 125 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.164983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.133528 restraints weight = 4313.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.133366 restraints weight = 3810.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.135113 restraints weight = 4224.984|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.4210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3848  Z= 0.164
  Angle     :  0.593  10.149   5285  Z= 0.295
  Chirality :  0.046   0.159    626
  Planarity :  0.004   0.047    652
  Dihedral  :  5.159  37.470    704
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 12.65 %
    Favored  : 84.41 %
  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:  0.01 (0.39), residues: 474
  helix:  3.72 (1.74), residues: 11
  sheet:  0.54 (0.36), residues: 191
  loop : -0.53 (0.39), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H 115 
 HIS   0.004   0.001   HIS A 245 
 PHE   0.020   0.002   PHE A  55 
 TYR   0.015   0.001   TYR A 265 
 ARG   0.003   0.001   ARG A 158 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00259 (    7)
  link_NAG-ASN         : angle       1.39626 (   21)
  link_BETA1-4         : bond        0.00521 (    2)
  link_BETA1-4         : angle       1.80543 (    6)
  hydrogen bonds       : bond        0.03154 (  116)
  hydrogen bonds       : angle       5.47419 (  288)
  SS BOND              : bond        0.00318 (    5)
  SS BOND              : angle       1.42495 (   10)
  covalent geometry    : bond        0.00389 ( 3834)
  covalent geometry    : angle       0.58192 ( 5248)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2358.21 seconds
wall clock time: 42 minutes 26.07 seconds (2546.07 seconds total)