Starting phenix.real_space_refine
on Thu Jul 24 13:09:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p5c_13198/07_2025/7p5c_13198.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p5c_13198/07_2025/7p5c_13198.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7p5c_13198/07_2025/7p5c_13198.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p5c_13198/07_2025/7p5c_13198.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p5c_13198/07_2025/7p5c_13198.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p5c_13198/07_2025/7p5c_13198.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
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      26      5.16       5
     C    4038      2.51       5
     N    1012      2.21       5
     O    1146      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6222
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3055
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 392, 3055
          Classifications: {'peptide': 392}
          Link IDs: {'PTRANS': 14, 'TRANS': 377}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3055
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 392, 3055
          Classifications: {'peptide': 392}
          Link IDs: {'PTRANS': 14, 'TRANS': 377}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 4.48, per 1000 atoms: 0.72
  Number of scatterers: 6222
  At special positions: 0
  Unit cell: (79.422, 71.61, 127.596, 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      26     16.00
     O    1146      8.00
     N    1012      7.00
     C    4038      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 271 " - pdb=" SG  CYS A 381 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 299 " - pdb=" SG  CYS A 366 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 271 " - pdb=" SG  CYS B 381 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 299 " - pdb=" SG  CYS B 366 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG A 601 " - " ASN A 144 "
      " NAG A 602 " - " ASN A 351 "
      " NAG B 601 " - " ASN B 144 "
      " NAG B 602 " - " ASN B 351 "
      " NAG C   1 " - " ASN A 126 "
      " NAG D   1 " - " ASN B 126 "
  Time building additional restraints: 2.49
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1464

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 0 sheets defined
      87.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 17
      removed outlier: 3.579A  pdb=" N   ARG A  17 " --> pdb=" O   SER A  13 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 36 through 66
      removed outlier: 3.608A  pdb=" N   ALA A  42 " --> pdb=" O   ASP A  38 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   LEU A  46 " --> pdb=" O   ALA A  42 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   ALA A  50 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   LEU A  51 " --> pdb=" O   GLY A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 158
      removed outlier: 4.456A  pdb=" N   GLU A 148 " --> pdb=" O   ASN A 144 " (cutoff:3.500A)
      Proline residue:  A 149  - end of helix
    Processing helix  chain 'A' and resid 161 through 185
      removed outlier: 3.595A  pdb=" N   ILE A 185 " --> pdb=" O   TYR A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 234
    Processing helix  chain 'A' and resid 235 through 273
      removed outlier: 4.042A  pdb=" N   ASP A 273 " --> pdb=" O   ASP A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 285
      removed outlier: 3.784A  pdb=" N   TYR A 277 " --> pdb=" O   ASP A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 299
    Processing helix  chain 'A' and resid 307 through 336
      removed outlier: 3.521A  pdb=" N   THR A 331 " --> pdb=" O   GLU A 327 " (cutoff:3.500A)
      Proline residue:  A 333  - end of helix
    Processing helix  chain 'A' and resid 339 through 364
      removed outlier: 4.286A  pdb=" N   GLY A 352 " --> pdb=" O   GLU A 348 " (cutoff:3.500A)
      removed outlier: 6.174A  pdb=" N   VAL A 355 " --> pdb=" O   ASN A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 409
      removed outlier: 4.283A  pdb=" N   LEU A 369 " --> pdb=" O   ASP A 365 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   GLU A 386 " --> pdb=" O   TYR A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 412
      No H-bonds generated for 'chain 'A' and resid 410 through 412'
    Processing helix  chain 'B' and resid 9 through 17
      removed outlier: 3.572A  pdb=" N   ARG B  17 " --> pdb=" O   SER B  13 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 66
      removed outlier: 3.583A  pdb=" N   ALA B  42 " --> pdb=" O   ASP B  38 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   ALA B  50 " --> pdb=" O   LEU B  46 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LEU B  51 " --> pdb=" O   GLY B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 145
    Processing helix  chain 'B' and resid 146 through 158
    Processing helix  chain 'B' and resid 161 through 184
    Processing helix  chain 'B' and resid 194 through 233
    Processing helix  chain 'B' and resid 235 through 273
      removed outlier: 3.547A  pdb=" N   PHE B 270 " --> pdb=" O   GLY B 266 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   ASP B 273 " --> pdb=" O   ASP B 269 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 273 through 285
      removed outlier: 3.879A  pdb=" N   TYR B 277 " --> pdb=" O   ASP B 273 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLU B 283 " --> pdb=" O   THR B 279 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 289 through 299
    Processing helix  chain 'B' and resid 307 through 330
    Processing helix  chain 'B' and resid 331 through 336
      removed outlier: 4.284A  pdb=" N   GLU B 335 " --> pdb=" O   THR B 331 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 364
    Processing helix  chain 'B' and resid 365 through 383
      removed outlier: 4.179A  pdb=" N   LEU B 369 " --> pdb=" O   ASP B 365 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LEU B 371 " --> pdb=" O   ARG B 367 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ASP B 383 " --> pdb=" O   GLY B 379 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 407
      removed outlier: 3.677A  pdb=" N   ALA B 399 " --> pdb=" O   SER B 395 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 408 through 413
      removed outlier: 3.684A  pdb=" N   TRP B 413 " --> pdb=" O   PRO B 410 " (cutoff:3.500A)

    548 hydrogen bonds defined for protein.
    1638 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: 1.71

  Time building geometry restraints manager: 2.32 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1950
        1.34 -     1.46: 1139
        1.46 -     1.58: 3249
        1.58 -     1.70: 0
        1.70 -     1.81: 32
  Bond restraints: 6370
  Sorted by residual:
  bond pdb=" C1  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.98e+00
  bond pdb=" C1  NAG A 602 "
       pdb=" O5  NAG A 602 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.76e+00
  bond pdb=" C1  NAG A 601 "
       pdb=" O5  NAG A 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.73e+00
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.72e+00
  bond pdb=" C1  NAG B 601 "
       pdb=" O5  NAG B 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.71e+00
  ... (remaining 6365 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 8572
        1.99 -     3.98: 111
        3.98 -     5.96: 26
        5.96 -     7.95: 5
        7.95 -     9.94: 2
  Bond angle restraints: 8716
  Sorted by residual:
  angle pdb=" C   PHE B  21 "
        pdb=" N   ASP B  22 "
        pdb=" CA  ASP B  22 "
      ideal   model   delta    sigma   weight residual
     121.54  130.23   -8.69 1.91e+00 2.74e-01 2.07e+01
  angle pdb=" CA  LEU A 250 "
        pdb=" CB  LEU A 250 "
        pdb=" CG  LEU A 250 "
      ideal   model   delta    sigma   weight residual
     116.30  126.24   -9.94 3.50e+00 8.16e-02 8.06e+00
  angle pdb=" N   VAL A 332 "
        pdb=" CA  VAL A 332 "
        pdb=" C   VAL A 332 "
      ideal   model   delta    sigma   weight residual
     108.88  114.50   -5.62 2.16e+00 2.14e-01 6.78e+00
  angle pdb=" N   ASP B  22 "
        pdb=" CA  ASP B  22 "
        pdb=" CB  ASP B  22 "
      ideal   model   delta    sigma   weight residual
     110.49  114.74   -4.25 1.69e+00 3.50e-01 6.33e+00
  angle pdb=" N   VAL B 332 "
        pdb=" CA  VAL B 332 "
        pdb=" C   VAL B 332 "
      ideal   model   delta    sigma   weight residual
     108.88  114.25   -5.37 2.16e+00 2.14e-01 6.18e+00
  ... (remaining 8711 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.69: 3364
       17.69 -    35.37: 358
       35.37 -    53.06: 58
       53.06 -    70.75: 19
       70.75 -    88.44: 3
  Dihedral angle restraints: 3802
    sinusoidal: 1526
      harmonic: 2276
  Sorted by residual:
  dihedral pdb=" CA  GLY A 352 "
           pdb=" C   GLY A 352 "
           pdb=" N   THR A 353 "
           pdb=" CA  THR A 353 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.50   20.50     0      5.00e+00 4.00e-02 1.68e+01
  dihedral pdb=" CA  HIS B 145 "
           pdb=" C   HIS B 145 "
           pdb=" N   THR B 146 "
           pdb=" CA  THR B 146 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.83   17.17     0      5.00e+00 4.00e-02 1.18e+01
  dihedral pdb=" CB  GLU A 335 "
           pdb=" CG  GLU A 335 "
           pdb=" CD  GLU A 335 "
           pdb=" OE1 GLU A 335 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.44  -88.44     1      3.00e+01 1.11e-03 1.04e+01
  ... (remaining 3799 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 976
       0.070 -    0.140: 76
       0.140 -    0.209: 0
       0.209 -    0.279: 1
       0.279 -    0.349: 1
  Chirality restraints: 1054
  Sorted by residual:
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN A 126 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.05   -0.35 2.00e-01 2.50e+01 3.04e+00
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN B 126 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.18   -0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CG  LEU A 293 "
            pdb=" CB  LEU A 293 "
            pdb=" CD1 LEU A 293 "
            pdb=" CD2 LEU A 293 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.45   -0.14 2.00e-01 2.50e+01 4.80e-01
  ... (remaining 1051 not shown)

  Planarity restraints: 1078
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A 381 "   -0.008 2.00e-02 2.50e+03   1.61e-02 2.59e+00
        pdb=" C   CYS A 381 "    0.028 2.00e-02 2.50e+03
        pdb=" O   CYS A 381 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   TYR A 382 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 352 "   -0.008 2.00e-02 2.50e+03   1.60e-02 2.56e+00
        pdb=" C   GLY A 352 "    0.028 2.00e-02 2.50e+03
        pdb=" O   GLY A 352 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   THR A 353 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 380 "   -0.007 2.00e-02 2.50e+03   1.34e-02 1.79e+00
        pdb=" C   PHE A 380 "    0.023 2.00e-02 2.50e+03
        pdb=" O   PHE A 380 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   CYS A 381 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1075 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1033
        2.76 -     3.29: 6302
        3.29 -     3.83: 10690
        3.83 -     4.36: 12122
        4.36 -     4.90: 21329
  Nonbonded interactions: 51476
  Sorted by model distance:
  nonbonded pdb=" O   VAL A  12 "
            pdb=" OG  SER A 268 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" OD1 ASN A 126 "
            pdb=" N2  NAG C   1 "
     model   vdw
     2.228 3.120
  nonbonded pdb=" OD1 ASP B 275 "
            pdb=" OH  TYR B 373 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OD1 ASP A 275 "
            pdb=" OH  TYR A 373 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" O   VAL B  12 "
            pdb=" OG  SER B 268 "
     model   vdw
     2.291 3.040
  ... (remaining 51471 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

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 individual isotropic
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:             0.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.720
  Find NCS groups from input model:        0.210
  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:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
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      :  0.004   0.038   6382  Z= 0.188
  Angle     :  0.619   9.939   8748  Z= 0.288
  Chirality :  0.041   0.349   1054
  Planarity :  0.003   0.026   1072
  Dihedral  : 14.521  88.436   2326
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  2.41 (0.29), residues: 776
  helix:  1.91 (0.20), residues: 646
  sheet:  None (None), residues: 0
  loop :  0.16 (0.56), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  10 
 HIS   0.003   0.001   HIS A  20 
 PHE   0.007   0.001   PHE A 394 
 TYR   0.010   0.001   TYR A 390 
 ARG   0.006   0.001   ARG B 170 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00926 (    6)
  link_NAG-ASN         : angle       2.77095 (   18)
  link_BETA1-4         : bond        0.00063 (    2)
  link_BETA1-4         : angle       1.62898 (    6)
  hydrogen bonds       : bond        0.17746 (  548)
  hydrogen bonds       : angle       6.04279 ( 1638)
  SS BOND              : bond        0.00426 (    4)
  SS BOND              : angle       1.42821 (    8)
  covalent geometry    : bond        0.00435 ( 6370)
  covalent geometry    : angle       0.60434 ( 8716)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.635 
Fit side-chains
   revert: symmetry clash
REVERT: A  106 TYR cc_start: 0.8214 (t80) cc_final: 0.7807 (t80)
REVERT: B  229 VAL cc_start: 0.8989 (t) cc_final: 0.8759 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.1819
  time to fit residues: 24.9820
Evaluate side-chains
  90 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 61 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
** A  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 375 GLN

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 = 0.127200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.105198 restraints weight = 6903.976|
|-----------------------------------------------------------------------------|
r_work (start): 0.3091 rms_B_bonded: 1.51
r_work: 0.2960 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2826 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.1009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6382  Z= 0.171
  Angle     :  0.610   9.119   8748  Z= 0.295
  Chirality :  0.039   0.221   1054
  Planarity :  0.004   0.036   1072
  Dihedral  :  5.486  51.135   1014
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  :  6.10 %
    Favored  : 92.84 %
  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:  3.27 (0.29), residues: 776
  helix:  2.57 (0.19), residues: 650
  sheet:  None (None), residues: 0
  loop : -0.04 (0.56), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  10 
 HIS   0.002   0.001   HIS A 116 
 PHE   0.007   0.001   PHE A 394 
 TYR   0.008   0.001   TYR A 120 
 ARG   0.005   0.000   ARG B 170 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00700 (    6)
  link_NAG-ASN         : angle       2.70569 (   18)
  link_BETA1-4         : bond        0.00157 (    2)
  link_BETA1-4         : angle       1.42516 (    6)
  hydrogen bonds       : bond        0.05241 (  548)
  hydrogen bonds       : angle       4.09141 ( 1638)
  SS BOND              : bond        0.00424 (    4)
  SS BOND              : angle       1.14101 (    8)
  covalent geometry    : bond        0.00390 ( 6370)
  covalent geometry    : angle       0.59684 ( 8716)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 106
  time to evaluate  : 0.626 
Fit side-chains
   revert: symmetry clash
REVERT: A  106 TYR cc_start: 0.8276 (t80) cc_final: 0.8040 (t80)
  outliers start: 7
  outliers final: 4
  residues processed: 107
  average time/residue: 0.1833
  time to fit residues: 26.0069
Evaluate side-chains
  103 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 99
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 GLU
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  375 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 40 optimal weight:    0.1980
   chunk 17 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   chunk 69 optimal weight:    0.7980
   chunk 12 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0870
   chunk 5 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9990
   chunk 55 optimal weight:    0.0570
   overall best weight:    0.3476

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

Flipped N/Q/H residues before XYZ refinement:
** A  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 375 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.130876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.108603 restraints weight = 6895.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.3134 rms_B_bonded: 1.53
r_work: 0.3004 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2868 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.1472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6382  Z= 0.118
  Angle     :  0.527   8.637   8748  Z= 0.255
  Chirality :  0.036   0.264   1054
  Planarity :  0.003   0.034   1072
  Dihedral  :  4.636  44.454   1014
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  9.45 %
    Favored  : 89.33 %
  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:  3.86 (0.28), residues: 776
  helix:  2.98 (0.19), residues: 652
  sheet:  None (None), residues: 0
  loop :  0.03 (0.56), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  11 
 HIS   0.002   0.000   HIS B 145 
 PHE   0.004   0.001   PHE A 394 
 TYR   0.025   0.001   TYR B 120 
 ARG   0.003   0.000   ARG B 170 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00524 (    6)
  link_NAG-ASN         : angle       2.49968 (   18)
  link_BETA1-4         : bond        0.00298 (    2)
  link_BETA1-4         : angle       1.24741 (    6)
  hydrogen bonds       : bond        0.04407 (  548)
  hydrogen bonds       : angle       3.66438 ( 1638)
  SS BOND              : bond        0.00272 (    4)
  SS BOND              : angle       0.80813 (    8)
  covalent geometry    : bond        0.00235 ( 6370)
  covalent geometry    : angle       0.51380 ( 8716)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 107
  time to evaluate  : 0.626 
Fit side-chains
REVERT: A   56 LEU cc_start: 0.7769 (tt) cc_final: 0.7460 (tp)
REVERT: B   22 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7831 (p0)
REVERT: B  127 ARG cc_start: 0.6694 (mmt180) cc_final: 0.6387 (mmt-90)
REVERT: B  344 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8459 (mm)
  outliers start: 8
  outliers final: 3
  residues processed: 110
  average time/residue: 0.1822
  time to fit residues: 26.1491
Evaluate side-chains
  108 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 103
  time to evaluate  : 0.620 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  375 GLN
Chi-restraints excluded: chain B residue   22 ASP
Chi-restraints excluded: chain B residue  148 GLU
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  375 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 28 optimal weight:    0.3980
   chunk 61 optimal weight:    0.5980
   chunk 2 optimal weight:    0.3980
   chunk 8 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 77 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A  16 HIS
** B  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.130165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.107878 restraints weight = 6898.970|
|-----------------------------------------------------------------------------|
r_work (start): 0.3124 rms_B_bonded: 1.52
r_work: 0.2994 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2857 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.2857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.1573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6382  Z= 0.134
  Angle     :  0.536   9.119   8748  Z= 0.257
  Chirality :  0.036   0.248   1054
  Planarity :  0.003   0.034   1072
  Dihedral  :  4.399  39.057   1014
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 10.82 %
    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:  3.99 (0.28), residues: 776
  helix:  3.08 (0.18), residues: 650
  sheet:  None (None), residues: 0
  loop :  0.08 (0.56), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  10 
 HIS   0.003   0.001   HIS A 370 
 PHE   0.006   0.001   PHE B 394 
 TYR   0.018   0.001   TYR B 120 
 ARG   0.004   0.000   ARG B 189 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00426 (    6)
  link_NAG-ASN         : angle       2.63737 (   18)
  link_BETA1-4         : bond        0.00254 (    2)
  link_BETA1-4         : angle       1.34246 (    6)
  hydrogen bonds       : bond        0.04335 (  548)
  hydrogen bonds       : angle       3.61104 ( 1638)
  SS BOND              : bond        0.00344 (    4)
  SS BOND              : angle       0.89676 (    8)
  covalent geometry    : bond        0.00296 ( 6370)
  covalent geometry    : angle       0.52121 ( 8716)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.803 
Fit side-chains
REVERT: A   35 GLU cc_start: 0.7797 (pm20) cc_final: 0.7576 (pm20)
REVERT: A   56 LEU cc_start: 0.8093 (tt) cc_final: 0.7830 (tp)
REVERT: B   22 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7908 (p0)
REVERT: B   35 GLU cc_start: 0.7690 (tt0) cc_final: 0.7367 (tt0)
REVERT: B  127 ARG cc_start: 0.6772 (mmt180) cc_final: 0.6428 (mmt-90)
REVERT: B  344 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8543 (mm)
  outliers start: 10
  outliers final: 6
  residues processed: 106
  average time/residue: 0.2327
  time to fit residues: 31.7986
Evaluate side-chains
  109 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 1.004 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain B residue   22 ASP
Chi-restraints excluded: chain B residue   30 SER
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  148 GLU
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  375 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 46 optimal weight:    0.5980
   chunk 41 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 72 optimal weight:    0.6980
   chunk 68 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 2 optimal weight:    0.3980
   chunk 44 optimal weight:    3.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 375 GLN
** B  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 375 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.127837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.105589 restraints weight = 6977.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.3093 rms_B_bonded: 1.52
r_work: 0.2965 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2829 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.1587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6382  Z= 0.162
  Angle     :  0.557   8.270   8748  Z= 0.267
  Chirality :  0.037   0.223   1054
  Planarity :  0.003   0.036   1072
  Dihedral  :  4.286  32.856   1014
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 11.74 %
    Favored  : 85.98 %
  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:  3.91 (0.28), residues: 776
  helix:  2.96 (0.18), residues: 660
  sheet:  None (None), residues: 0
  loop :  0.21 (0.60), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  10 
 HIS   0.002   0.001   HIS A 116 
 PHE   0.009   0.001   PHE B 394 
 TYR   0.017   0.001   TYR B 120 
 ARG   0.005   0.000   ARG A 330 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00314 (    6)
  link_NAG-ASN         : angle       2.75580 (   18)
  link_BETA1-4         : bond        0.00254 (    2)
  link_BETA1-4         : angle       1.42659 (    6)
  hydrogen bonds       : bond        0.04438 (  548)
  hydrogen bonds       : angle       3.64426 ( 1638)
  SS BOND              : bond        0.00460 (    4)
  SS BOND              : angle       1.02962 (    8)
  covalent geometry    : bond        0.00379 ( 6370)
  covalent geometry    : angle       0.54192 ( 8716)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.633 
Fit side-chains
REVERT: A   35 GLU cc_start: 0.7820 (pm20) cc_final: 0.7571 (pm20)
REVERT: A   56 LEU cc_start: 0.8066 (tt) cc_final: 0.7807 (tp)
REVERT: A   95 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6302 (mp)
REVERT: B   22 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7976 (p0)
REVERT: B   35 GLU cc_start: 0.7847 (tt0) cc_final: 0.7601 (tt0)
REVERT: B  344 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8554 (mm)
  outliers start: 15
  outliers final: 11
  residues processed: 106
  average time/residue: 0.2092
  time to fit residues: 28.7233
Evaluate side-chains
  110 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  281 MET
Chi-restraints excluded: chain A residue  375 GLN
Chi-restraints excluded: chain B residue   18 LEU
Chi-restraints excluded: chain B residue   22 ASP
Chi-restraints excluded: chain B residue   30 SER
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  148 GLU
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  375 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 50 optimal weight:    3.9990
   chunk 25 optimal weight:    0.0570
   chunk 57 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.7300

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

Flipped N/Q/H residues before XYZ refinement:
** B  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.128889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.106557 restraints weight = 6842.949|
|-----------------------------------------------------------------------------|
r_work (start): 0.3104 rms_B_bonded: 1.51
r_work: 0.2975 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2840 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.1663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6382  Z= 0.143
  Angle     :  0.541   8.019   8748  Z= 0.260
  Chirality :  0.036   0.218   1054
  Planarity :  0.003   0.036   1072
  Dihedral  :  4.098  25.682   1014
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 12.65 %
    Favored  : 85.37 %
  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:  4.01 (0.28), residues: 776
  helix:  3.03 (0.18), residues: 660
  sheet:  None (None), residues: 0
  loop :  0.19 (0.60), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  10 
 HIS   0.004   0.001   HIS A 370 
 PHE   0.006   0.001   PHE B 394 
 TYR   0.016   0.001   TYR B 120 
 ARG   0.006   0.000   ARG A 330 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00256 (    6)
  link_NAG-ASN         : angle       2.63516 (   18)
  link_BETA1-4         : bond        0.00162 (    2)
  link_BETA1-4         : angle       1.35168 (    6)
  hydrogen bonds       : bond        0.04349 (  548)
  hydrogen bonds       : angle       3.59455 ( 1638)
  SS BOND              : bond        0.00379 (    4)
  SS BOND              : angle       0.95999 (    8)
  covalent geometry    : bond        0.00324 ( 6370)
  covalent geometry    : angle       0.52670 ( 8716)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.715 
Fit side-chains
REVERT: A   35 GLU cc_start: 0.7873 (pm20) cc_final: 0.7596 (pm20)
REVERT: A   56 LEU cc_start: 0.8145 (tt) cc_final: 0.7846 (tp)
REVERT: A   95 LEU cc_start: 0.6791 (OUTLIER) cc_final: 0.6318 (mp)
REVERT: B   22 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7956 (p0)
REVERT: B  127 ARG cc_start: 0.6859 (mmt180) cc_final: 0.6523 (mmt-90)
REVERT: B  344 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8561 (mm)
  outliers start: 13
  outliers final: 8
  residues processed: 101
  average time/residue: 0.2298
  time to fit residues: 29.6297
Evaluate side-chains
  107 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  281 MET
Chi-restraints excluded: chain B residue   18 LEU
Chi-restraints excluded: chain B residue   22 ASP
Chi-restraints excluded: chain B residue   30 SER
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  148 GLU
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  344 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   chunk 51 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 55 optimal weight:    0.7980
   chunk 67 optimal weight:    0.7980
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 375 GLN
** B  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 375 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.128479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.106051 restraints weight = 6859.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.3103 rms_B_bonded: 1.53
r_work: 0.2978 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2845 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.1724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6382  Z= 0.150
  Angle     :  0.542   7.666   8748  Z= 0.260
  Chirality :  0.037   0.201   1054
  Planarity :  0.003   0.037   1072
  Dihedral  :  4.014  22.770   1014
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 13.57 %
    Favored  : 83.99 %
  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:  4.00 (0.28), residues: 776
  helix:  3.01 (0.18), residues: 662
  sheet:  None (None), residues: 0
  loop :  0.23 (0.61), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  10 
 HIS   0.002   0.001   HIS B  20 
 PHE   0.008   0.001   PHE B 394 
 TYR   0.016   0.001   TYR B 120 
 ARG   0.007   0.000   ARG A 330 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00238 (    6)
  link_NAG-ASN         : angle       2.57341 (   18)
  link_BETA1-4         : bond        0.00209 (    2)
  link_BETA1-4         : angle       1.38224 (    6)
  hydrogen bonds       : bond        0.04367 (  548)
  hydrogen bonds       : angle       3.58690 ( 1638)
  SS BOND              : bond        0.00421 (    4)
  SS BOND              : angle       1.01451 (    8)
  covalent geometry    : bond        0.00347 ( 6370)
  covalent geometry    : angle       0.52772 ( 8716)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.697 
Fit side-chains
REVERT: A   35 GLU cc_start: 0.7849 (pm20) cc_final: 0.7406 (pm20)
REVERT: A   56 LEU cc_start: 0.8198 (tt) cc_final: 0.7898 (tp)
REVERT: A   95 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6377 (mp)
REVERT: B   22 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7981 (p0)
REVERT: B  127 ARG cc_start: 0.6958 (mmt180) cc_final: 0.6607 (mmt-90)
REVERT: B  152 GLN cc_start: 0.7591 (mt0) cc_final: 0.7288 (mm-40)
REVERT: B  344 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8609 (mm)
  outliers start: 16
  outliers final: 9
  residues processed: 102
  average time/residue: 0.2173
  time to fit residues: 28.4000
Evaluate side-chains
  102 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  148 GLU
Chi-restraints excluded: chain B residue   18 LEU
Chi-restraints excluded: chain B residue   22 ASP
Chi-restraints excluded: chain B residue   30 SER
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  148 GLU
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  344 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
A 375 GLN
** B  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.126796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.104401 restraints weight = 6859.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3070 rms_B_bonded: 1.52
r_work: 0.2941 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2808 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.1715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6382  Z= 0.180
  Angle     :  0.570   7.624   8748  Z= 0.273
  Chirality :  0.038   0.181   1054
  Planarity :  0.003   0.038   1072
  Dihedral  :  4.130  23.568   1014
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 14.48 %
    Favored  : 83.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.84 (0.28), residues: 776
  helix:  2.89 (0.18), residues: 662
  sheet:  None (None), residues: 0
  loop :  0.26 (0.61), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  10 
 HIS   0.003   0.001   HIS B  20 
 PHE   0.010   0.001   PHE B 394 
 TYR   0.015   0.001   TYR B 120 
 ARG   0.004   0.000   ARG A 330 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00210 (    6)
  link_NAG-ASN         : angle       2.62953 (   18)
  link_BETA1-4         : bond        0.00128 (    2)
  link_BETA1-4         : angle       1.51844 (    6)
  hydrogen bonds       : bond        0.04536 (  548)
  hydrogen bonds       : angle       3.66088 ( 1638)
  SS BOND              : bond        0.00523 (    4)
  SS BOND              : angle       1.14004 (    8)
  covalent geometry    : bond        0.00426 ( 6370)
  covalent geometry    : angle       0.55618 ( 8716)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.634 
Fit side-chains
REVERT: A   35 GLU cc_start: 0.7848 (pm20) cc_final: 0.7374 (pm20)
REVERT: A   56 LEU cc_start: 0.8119 (tt) cc_final: 0.7820 (tp)
REVERT: A   95 LEU cc_start: 0.6781 (OUTLIER) cc_final: 0.6300 (mp)
REVERT: B  127 ARG cc_start: 0.6749 (mmt180) cc_final: 0.6424 (mmt-90)
REVERT: B  152 GLN cc_start: 0.7573 (mt0) cc_final: 0.7201 (mm-40)
REVERT: B  344 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8545 (mm)
  outliers start: 15
  outliers final: 9
  residues processed: 101
  average time/residue: 0.2003
  time to fit residues: 26.0046
Evaluate side-chains
  101 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  148 GLU
Chi-restraints excluded: chain B residue   18 LEU
Chi-restraints excluded: chain B residue   30 SER
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  148 GLU
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  344 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   chunk 12 optimal weight:    0.4980
   chunk 42 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 73 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A 375 GLN
** B  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.127304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.104494 restraints weight = 6972.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 1.56
r_work: 0.2951 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2815 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.2815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.1739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6382  Z= 0.170
  Angle     :  0.569   9.230   8748  Z= 0.273
  Chirality :  0.037   0.188   1054
  Planarity :  0.003   0.038   1072
  Dihedral  :  4.081  23.514   1014
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 15.09 %
    Favored  : 82.77 %
  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:  3.82 (0.28), residues: 776
  helix:  2.88 (0.18), residues: 662
  sheet:  None (None), residues: 0
  loop :  0.21 (0.61), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  10 
 HIS   0.004   0.001   HIS B  20 
 PHE   0.009   0.001   PHE B 394 
 TYR   0.015   0.001   TYR B 120 
 ARG   0.005   0.000   ARG A 330 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00179 (    6)
  link_NAG-ASN         : angle       2.58340 (   18)
  link_BETA1-4         : bond        0.00134 (    2)
  link_BETA1-4         : angle       1.54659 (    6)
  hydrogen bonds       : bond        0.04492 (  548)
  hydrogen bonds       : angle       3.65062 ( 1638)
  SS BOND              : bond        0.00478 (    4)
  SS BOND              : angle       1.10296 (    8)
  covalent geometry    : bond        0.00401 ( 6370)
  covalent geometry    : angle       0.55516 ( 8716)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.700 
Fit side-chains
REVERT: A   35 GLU cc_start: 0.7868 (pm20) cc_final: 0.7353 (pm20)
REVERT: A   56 LEU cc_start: 0.8112 (tt) cc_final: 0.7819 (tp)
REVERT: A   95 LEU cc_start: 0.6751 (OUTLIER) cc_final: 0.6270 (mp)
REVERT: B  127 ARG cc_start: 0.6722 (mmt180) cc_final: 0.6399 (mmt-90)
REVERT: B  344 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8536 (mm)
  outliers start: 14
  outliers final: 10
  residues processed: 97
  average time/residue: 0.3003
  time to fit residues: 37.3342
Evaluate side-chains
  101 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  148 GLU
Chi-restraints excluded: chain B residue   18 LEU
Chi-restraints excluded: chain B residue   30 SER
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  148 GLU
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  344 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 16 optimal weight:    0.0060
   chunk 73 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 70 optimal weight:    0.0670
   chunk 65 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.5534

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

Flipped N/Q/H residues before XYZ refinement:
** B  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.129341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.106938 restraints weight = 6971.929|
|-----------------------------------------------------------------------------|
r_work (start): 0.3104 rms_B_bonded: 1.55
r_work: 0.2976 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2841 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.2841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.1858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6382  Z= 0.126
  Angle     :  0.527   8.852   8748  Z= 0.254
  Chirality :  0.036   0.201   1054
  Planarity :  0.003   0.037   1072
  Dihedral  :  3.845  22.741   1014
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 15.85 %
    Favored  : 82.32 %
  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:  4.11 (0.29), residues: 776
  helix:  3.11 (0.18), residues: 660
  sheet:  None (None), residues: 0
  loop :  0.17 (0.60), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  67 
 HIS   0.002   0.001   HIS B  20 
 PHE   0.005   0.001   PHE A 187 
 TYR   0.016   0.001   TYR B 120 
 ARG   0.006   0.000   ARG A 330 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00234 (    6)
  link_NAG-ASN         : angle       2.31716 (   18)
  link_BETA1-4         : bond        0.00198 (    2)
  link_BETA1-4         : angle       1.39343 (    6)
  hydrogen bonds       : bond        0.04220 (  548)
  hydrogen bonds       : angle       3.51029 ( 1638)
  SS BOND              : bond        0.00335 (    4)
  SS BOND              : angle       0.88318 (    8)
  covalent geometry    : bond        0.00275 ( 6370)
  covalent geometry    : angle       0.51562 ( 8716)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.713 
Fit side-chains
REVERT: A   35 GLU cc_start: 0.7802 (pm20) cc_final: 0.7358 (pm20)
REVERT: A   56 LEU cc_start: 0.8126 (tt) cc_final: 0.7819 (tp)
REVERT: A   95 LEU cc_start: 0.6836 (OUTLIER) cc_final: 0.6363 (mp)
REVERT: A  372 ASP cc_start: 0.7579 (m-30) cc_final: 0.7378 (m-30)
REVERT: B  127 ARG cc_start: 0.6786 (mmt180) cc_final: 0.6484 (mmt-90)
REVERT: B  330 ARG cc_start: 0.7714 (ptm-80) cc_final: 0.7378 (ptp90)
REVERT: B  344 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8517 (mm)
  outliers start: 12
  outliers final: 8
  residues processed: 102
  average time/residue: 0.2639
  time to fit residues: 34.2795
Evaluate side-chains
  103 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain B residue   18 LEU
Chi-restraints excluded: chain B residue   30 SER
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  148 GLU
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  344 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 6 optimal weight:    0.0170
   chunk 75 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.8820

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

Flipped N/Q/H residues before XYZ refinement:
** B  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.127858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.105483 restraints weight = 7040.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.3086 rms_B_bonded: 1.55
r_work: 0.2960 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2826 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.1815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6382  Z= 0.155
  Angle     :  0.558  10.744   8748  Z= 0.266
  Chirality :  0.037   0.187   1054
  Planarity :  0.003   0.037   1072
  Dihedral  :  3.929  23.097   1014
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 16.62 %
    Favored  : 81.71 %
  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:  4.00 (0.29), residues: 776
  helix:  3.03 (0.18), residues: 660
  sheet:  None (None), residues: 0
  loop :  0.18 (0.60), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  67 
 HIS   0.002   0.001   HIS B  20 
 PHE   0.008   0.001   PHE B 394 
 TYR   0.015   0.001   TYR B 120 
 ARG   0.007   0.000   ARG A 330 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00182 (    6)
  link_NAG-ASN         : angle       2.41760 (   18)
  link_BETA1-4         : bond        0.00160 (    2)
  link_BETA1-4         : angle       1.55991 (    6)
  hydrogen bonds       : bond        0.04373 (  548)
  hydrogen bonds       : angle       3.56100 ( 1638)
  SS BOND              : bond        0.00451 (    4)
  SS BOND              : angle       1.04384 (    8)
  covalent geometry    : bond        0.00360 ( 6370)
  covalent geometry    : angle       0.54597 ( 8716)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3227.80 seconds
wall clock time: 57 minutes 50.51 seconds (3470.51 seconds total)