Starting phenix.real_space_refine
on Thu Jul  2 03:11:34 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7p5c_13198/07_2026/7p5c_13198.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p5c_13198/07_2026/7p5c_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 {
    restraint_files = "/net/cci-nas-00/data/ceres_data/7p5c_13198/07_2026/7p5c_13198.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7p5c_13198/07_2026/7p5c_13198.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p5c_13198/07_2026/7p5c_13198.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p5c_13198/07_2026/7p5c_13198.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7p5c_13198/07_2026/7p5c_13198.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p5c_13198/07_2026/7p5c_13198.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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 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 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 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 chiralities: 2
  Time building chain proxies: 1.71, per 1000 atoms: 0.27
  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: 0.63
  Conformation dependent library (CDL) restraints added in 406.6 milliseconds
  

  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: 0.15
  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: 1.02

  Time building geometry restraints manager: 0.80 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: 3222
       17.69 -    35.37: 339
       35.37 -    53.06: 53
       53.06 -    70.75: 17
       70.75 -    88.44: 3
  Dihedral angle restraints: 3634
    sinusoidal: 1358
      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 3631 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: 0.01
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:             0.970
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.870
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.010
  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:1.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
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  : 14.626  88.436   2158
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.006   0.001   ARG B 170 
 TYR   0.010   0.001   TYR A 390 
 PHE   0.007   0.001   PHE A 394 
 TRP   0.008   0.001   TRP A  10 
 HIS   0.003   0.001   HIS A  20 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00435 /  0.19 ( 6370)
  covalent geometry    : angle       0.60434 /  0.28 ( 8716)
  SS BOND              : bond        0.00426 /  0.19 (    4)
  SS BOND              : angle       1.42821 /  0.77 (    8)
  hydrogen bonds       : bond        0.17746 / 11.79 (  548)
  hydrogen bonds       : angle       6.04279 /  4.52 ( 1638)
  link_BETA1-4         : bond        0.00063 /  0.03 (    2)
  link_BETA1-4         : angle       1.62898 /  0.81 (    6)
  link_NAG-ASN         : bond        0.00926 /  0.48 (    6)
  link_NAG-ASN         : angle       2.77095 /  1.65 (   18)

*********************** 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  : 0.213 
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: 0.0773
  time to fit residues: 10.6952
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  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3368 r_free = 0.3368 target = 0.127921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.105760 restraints weight = 6983.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.3101 rms_B_bonded: 1.53
r_work: 0.2970 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2835 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.2835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.1041

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= 0.159
  Angle     :  0.600   8.971   8748  Z= 0.290
  Chirality :  0.038   0.212   1054
  Planarity :  0.004   0.035   1072
  Dihedral  :  3.766  19.935    846
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  6.25 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.32 (0.29), residues: 776
  helix:  2.60 (0.19), residues: 650
  sheet:  None (None), residues: 0
  loop : -0.06 (0.56), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 170 
 TYR   0.008   0.001   TYR A 120 
 PHE   0.007   0.001   PHE A 394 
 TRP   0.006   0.001   TRP B 207 
 HIS   0.002   0.001   HIS B 116 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00354 /  0.16 ( 6370)
  covalent geometry    : angle       0.58673 /  0.29 ( 8716)
  SS BOND              : bond        0.00383 /  0.18 (    4)
  SS BOND              : angle       1.07326 /  0.58 (    8)
  hydrogen bonds       : bond        0.05181 /  3.46 (  548)
  hydrogen bonds       : angle       4.05565 /  2.96 ( 1638)
  link_BETA1-4         : bond        0.00093 /  0.04 (    2)
  link_BETA1-4         : angle       1.26602 /  0.65 (    6)
  link_NAG-ASN         : bond        0.00691 /  0.36 (    6)
  link_NAG-ASN         : angle       2.69186 /  1.69 (   18)

*********************** 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
  111 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 105
  time to evaluate  : 0.220 
Fit side-chains
  outliers start: 6
  outliers final: 2
  residues processed: 106
  average time/residue: 0.0796
  time to fit residues: 11.3052
Evaluate side-chains
  98 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 96
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 25 optimal weight:    0.6980
   chunk 60 optimal weight:    0.0040
   chunk 33 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 57 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 77 optimal weight:    0.0050
   chunk 27 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    0.4806

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3391 r_free = 0.3391 target = 0.130160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.107991 restraints weight = 6910.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3126 rms_B_bonded: 1.52
r_work: 0.2998 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2863 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.1437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6382  Z= 0.129
  Angle     :  0.539   8.444   8748  Z= 0.260
  Chirality :  0.036   0.164   1054
  Planarity :  0.003   0.033   1072
  Dihedral  :  3.616  19.913    846
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  9.15 %
    Favored  : 89.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.79 (0.28), residues: 776
  helix:  2.93 (0.19), residues: 652
  sheet:  None (None), residues: 0
  loop :  0.04 (0.56), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 170 
 TYR   0.023   0.001   TYR B 120 
 PHE   0.006   0.001   PHE A 394 
 TRP   0.007   0.001   TRP A  11 
 HIS   0.002   0.001   HIS B 124 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.13 ( 6370)
  covalent geometry    : angle       0.52565 /  0.26 ( 8716)
  SS BOND              : bond        0.00319 /  0.15 (    4)
  SS BOND              : angle       0.86851 /  0.48 (    8)
  hydrogen bonds       : bond        0.04479 /  2.99 (  548)
  hydrogen bonds       : angle       3.69932 /  2.69 ( 1638)
  link_BETA1-4         : bond        0.00197 /  0.10 (    2)
  link_BETA1-4         : angle       1.28108 /  0.68 (    6)
  link_NAG-ASN         : bond        0.00834 /  0.44 (    6)
  link_NAG-ASN         : angle       2.50728 /  1.62 (   18)

*********************** 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
  114 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 108
  time to evaluate  : 0.231 
Fit side-chains
REVERT: A   56 LEU cc_start: 0.7798 (tt) cc_final: 0.7493 (tp)
REVERT: B   22 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7840 (p0)
REVERT: B   35 GLU cc_start: 0.7568 (tt0) cc_final: 0.7295 (tt0)
REVERT: B  344 LEU cc_start: 0.8727 (mm) cc_final: 0.8489 (mm)
  outliers start: 6
  outliers final: 3
  residues processed: 110
  average time/residue: 0.0781
  time to fit residues: 11.4896
Evaluate side-chains
  108 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 104
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
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  375 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 4 optimal weight:    0.5980
   chunk 29 optimal weight:    2.9990
   chunk 22 optimal weight:    0.5980
   chunk 55 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  16 HIS
** 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 = 0.3362 r_free = 0.3362 target = 0.127750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.105486 restraints weight = 6959.049|
|-----------------------------------------------------------------------------|
r_work (start): 0.3091 rms_B_bonded: 1.51
r_work: 0.2960 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2824 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.2824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.1534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6382  Z= 0.171
  Angle     :  0.575   9.063   8748  Z= 0.275
  Chirality :  0.038   0.187   1054
  Planarity :  0.003   0.035   1072
  Dihedral  :  3.687  20.184    846
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 10.06 %
    Favored  : 87.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.75 (0.28), residues: 776
  helix:  2.85 (0.18), residues: 660
  sheet:  None (None), residues: 0
  loop :  0.15 (0.60), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 189 
 TYR   0.016   0.001   TYR A 373 
 PHE   0.009   0.001   PHE B 394 
 TRP   0.008   0.001   TRP A  10 
 HIS   0.005   0.001   HIS A 370 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00403 /  0.17 ( 6370)
  covalent geometry    : angle       0.56055 /  0.27 ( 8716)
  SS BOND              : bond        0.00469 /  0.22 (    4)
  SS BOND              : angle       1.05692 /  0.58 (    8)
  hydrogen bonds       : bond        0.04558 /  3.05 (  548)
  hydrogen bonds       : angle       3.72645 /  2.70 ( 1638)
  link_BETA1-4         : bond        0.00268 /  0.14 (    2)
  link_BETA1-4         : angle       1.31115 /  0.66 (    6)
  link_NAG-ASN         : bond        0.00286 /  0.14 (    6)
  link_NAG-ASN         : angle       2.77995 /  1.79 (   18)

*********************** 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
  104 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.223 
Fit side-chains
REVERT: A   35 GLU cc_start: 0.7793 (pm20) cc_final: 0.7574 (pm20)
REVERT: A   56 LEU cc_start: 0.8042 (tt) cc_final: 0.7783 (tp)
REVERT: B   35 GLU cc_start: 0.7717 (tt0) cc_final: 0.7396 (tt0)
REVERT: B  127 ARG cc_start: 0.6764 (mmt180) cc_final: 0.6490 (mmt-90)
REVERT: B  344 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8510 (mm)
  outliers start: 14
  outliers final: 11
  residues processed: 99
  average time/residue: 0.0826
  time to fit residues: 10.5523
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  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
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   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
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 19 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 46 optimal weight:    0.5980
   chunk 42 optimal weight:    0.0770
   chunk 62 optimal weight:    0.6980
   chunk 71 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.5338

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3386 r_free = 0.3386 target = 0.129701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.107154 restraints weight = 7009.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.3110 rms_B_bonded: 1.53
r_work: 0.2984 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2849 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.1695

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= 0.128
  Angle     :  0.532   8.423   8748  Z= 0.256
  Chirality :  0.036   0.202   1054
  Planarity :  0.003   0.035   1072
  Dihedral  :  3.606  20.110    846
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 11.59 %
    Favored  : 86.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.98 (0.28), residues: 776
  helix:  3.01 (0.18), residues: 660
  sheet:  None (None), residues: 0
  loop :  0.18 (0.60), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 330 
 TYR   0.016   0.001   TYR A 373 
 PHE   0.005   0.001   PHE B 394 
 TRP   0.007   0.001   TRP A  11 
 HIS   0.004   0.001   HIS B 370 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.13 ( 6370)
  covalent geometry    : angle       0.51816 /  0.25 ( 8716)
  SS BOND              : bond        0.00315 /  0.15 (    4)
  SS BOND              : angle       0.88490 /  0.49 (    8)
  hydrogen bonds       : bond        0.04286 /  2.87 (  548)
  hydrogen bonds       : angle       3.58207 /  2.60 ( 1638)
  link_BETA1-4         : bond        0.00323 /  0.16 (    2)
  link_BETA1-4         : angle       1.20196 /  0.59 (    6)
  link_NAG-ASN         : bond        0.00296 /  0.16 (    6)
  link_NAG-ASN         : angle       2.60719 /  1.68 (   18)

*********************** 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
  115 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.228 
Fit side-chains
REVERT: A   35 GLU cc_start: 0.7791 (pm20) cc_final: 0.7572 (pm20)
REVERT: A   56 LEU cc_start: 0.8070 (tt) cc_final: 0.7809 (tp)
REVERT: A   95 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.6287 (mp)
REVERT: B   22 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7952 (p0)
REVERT: B   35 GLU cc_start: 0.7844 (tt0) cc_final: 0.7549 (tt0)
REVERT: B  127 ARG cc_start: 0.6830 (mmt180) cc_final: 0.6494 (mmt-90)
REVERT: B  344 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8521 (mm)
  outliers start: 12
  outliers final: 8
  residues processed: 108
  average time/residue: 0.0897
  time to fit residues: 12.4537
Evaluate side-chains
  111 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
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   22 ASP
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  259 LEU
Chi-restraints excluded: chain B residue  344 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 59 optimal weight:    0.1980
   chunk 31 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 9 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9980
   chunk 73 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 375 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.129227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.106821 restraints weight = 6887.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 1.53
r_work: 0.2990 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2856 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.1721

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     :  0.532   8.010   8748  Z= 0.256
  Chirality :  0.036   0.194   1054
  Planarity :  0.003   0.035   1072
  Dihedral  :  3.588  19.979    846
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 12.80 %
    Favored  : 85.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.04 (0.28), residues: 776
  helix:  3.05 (0.18), residues: 660
  sheet:  None (None), residues: 0
  loop :  0.21 (0.60), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 330 
 TYR   0.015   0.001   TYR A 373 
 PHE   0.006   0.001   PHE B 394 
 TRP   0.007   0.001   TRP A  10 
 HIS   0.003   0.001   HIS A 370 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00299 /  0.13 ( 6370)
  covalent geometry    : angle       0.51853 /  0.25 ( 8716)
  SS BOND              : bond        0.00372 /  0.18 (    4)
  SS BOND              : angle       0.91494 /  0.50 (    8)
  hydrogen bonds       : bond        0.04271 /  2.86 (  548)
  hydrogen bonds       : angle       3.55555 /  2.57 ( 1638)
  link_BETA1-4         : bond        0.00344 /  0.17 (    2)
  link_BETA1-4         : angle       1.23434 /  0.61 (    6)
  link_NAG-ASN         : bond        0.00262 /  0.14 (    6)
  link_NAG-ASN         : angle       2.51461 /  1.57 (   18)

*********************** 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
  110 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.202 
Fit side-chains
REVERT: A   35 GLU cc_start: 0.7869 (pm20) cc_final: 0.7644 (pm20)
REVERT: A   56 LEU cc_start: 0.8176 (tt) cc_final: 0.7880 (tp)
REVERT: A   95 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6357 (mp)
REVERT: B   22 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7985 (p0)
REVERT: B  127 ARG cc_start: 0.6932 (mmt180) cc_final: 0.6565 (mmt-90)
REVERT: B  339 THR cc_start: 0.8722 (p) cc_final: 0.8481 (p)
REVERT: B  344 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8563 (mm)
  outliers start: 14
  outliers final: 10
  residues processed: 103
  average time/residue: 0.0753
  time to fit residues: 10.0510
Evaluate side-chains
  109 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
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 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   44 LEU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   chunk 70 optimal weight:    0.7980
   chunk 10 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 66 optimal weight:    0.0980
   chunk 30 optimal weight:    0.8980
   chunk 75 optimal weight:    2.9990
   chunk 67 optimal weight:    0.1980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3387 r_free = 0.3387 target = 0.129942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.107520 restraints weight = 6897.436|
|-----------------------------------------------------------------------------|
r_work (start): 0.3124 rms_B_bonded: 1.53
r_work: 0.3000 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2867 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.2867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.1769

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= 0.122
  Angle     :  0.518   7.836   8748  Z= 0.249
  Chirality :  0.035   0.190   1054
  Planarity :  0.003   0.036   1072
  Dihedral  :  3.560  20.044    846
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 13.41 %
    Favored  : 84.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.17 (0.28), residues: 776
  helix:  3.14 (0.18), residues: 660
  sheet:  None (None), residues: 0
  loop :  0.21 (0.60), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 330 
 TYR   0.019   0.001   TYR B 373 
 PHE   0.005   0.001   PHE B 394 
 TRP   0.007   0.001   TRP A  11 
 HIS   0.003   0.001   HIS B 370 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.12 ( 6370)
  covalent geometry    : angle       0.50634 /  0.25 ( 8716)
  SS BOND              : bond        0.00328 /  0.16 (    4)
  SS BOND              : angle       0.86008 /  0.48 (    8)
  hydrogen bonds       : bond        0.04197 /  2.81 (  548)
  hydrogen bonds       : angle       3.49747 /  2.53 ( 1638)
  link_BETA1-4         : bond        0.00224 /  0.11 (    2)
  link_BETA1-4         : angle       1.18486 /  0.59 (    6)
  link_NAG-ASN         : bond        0.00251 /  0.13 (    6)
  link_NAG-ASN         : angle       2.38309 /  1.46 (   18)

*********************** 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
  113 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.233 
Fit side-chains
REVERT: A   35 GLU cc_start: 0.7855 (pm20) cc_final: 0.7618 (pm20)
REVERT: A   56 LEU cc_start: 0.8192 (tt) cc_final: 0.7896 (tp)
REVERT: A   95 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.6435 (mp)
REVERT: B   22 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7946 (p0)
REVERT: B  127 ARG cc_start: 0.6916 (mmt180) cc_final: 0.6544 (mmt-90)
REVERT: B  152 GLN cc_start: 0.7458 (mt0) cc_final: 0.7207 (mm-40)
REVERT: B  344 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8559 (mm)
REVERT: B  372 ASP cc_start: 0.7895 (m-30) cc_final: 0.7501 (m-30)
  outliers start: 14
  outliers final: 7
  residues processed: 105
  average time/residue: 0.0819
  time to fit residues: 11.1391
Evaluate side-chains
  101 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 91
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   44 LEU
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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 64 optimal weight:    0.3980
   chunk 69 optimal weight:    3.9990
   chunk 56 optimal weight:    0.7980
   chunk 52 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 46 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3375 r_free = 0.3375 target = 0.128906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.106509 restraints weight = 6949.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.3103 rms_B_bonded: 1.53
r_work: 0.2977 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2843 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.1785

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= 0.144
  Angle     :  0.534   7.590   8748  Z= 0.256
  Chirality :  0.036   0.176   1054
  Planarity :  0.003   0.036   1072
  Dihedral  :  3.593  20.028    846
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 14.33 %
    Favored  : 83.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.09 (0.28), residues: 776
  helix:  3.08 (0.18), residues: 660
  sheet:  None (None), residues: 0
  loop :  0.22 (0.60), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 189 
 TYR   0.023   0.001   TYR B 373 
 PHE   0.007   0.001   PHE B 394 
 TRP   0.007   0.001   TRP A  10 
 HIS   0.002   0.001   HIS B  20 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00330 /  0.14 ( 6370)
  covalent geometry    : angle       0.52185 /  0.25 ( 8716)
  SS BOND              : bond        0.00408 /  0.19 (    4)
  SS BOND              : angle       0.96476 /  0.53 (    8)
  hydrogen bonds       : bond        0.04306 /  2.89 (  548)
  hydrogen bonds       : angle       3.53130 /  2.55 ( 1638)
  link_BETA1-4         : bond        0.00277 /  0.14 (    2)
  link_BETA1-4         : angle       1.28479 /  0.63 (    6)
  link_NAG-ASN         : bond        0.00201 /  0.10 (    6)
  link_NAG-ASN         : angle       2.40931 /  1.43 (   18)

*********************** 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
  108 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.185 
Fit side-chains
REVERT: A   35 GLU cc_start: 0.7873 (pm20) cc_final: 0.7414 (pm20)
REVERT: A   56 LEU cc_start: 0.8129 (tt) cc_final: 0.7842 (tp)
REVERT: A   95 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6231 (mp)
REVERT: B   22 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7942 (p0)
REVERT: B  152 GLN cc_start: 0.7549 (mt0) cc_final: 0.7205 (mm-40)
REVERT: B  330 ARG cc_start: 0.7749 (ptm-80) cc_final: 0.7369 (ptp90)
REVERT: B  344 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8473 (mm)
REVERT: B  372 ASP cc_start: 0.7579 (m-30) cc_final: 0.7217 (m-30)
  outliers start: 15
  outliers final: 8
  residues processed: 101
  average time/residue: 0.0929
  time to fit residues: 11.9666
Evaluate side-chains
  103 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   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  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 56 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 58 optimal weight:    0.6980
   chunk 52 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 25 optimal weight:    0.6980
   chunk 51 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3372 r_free = 0.3372 target = 0.128616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.106248 restraints weight = 6990.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 1.53
r_work: 0.2990 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2856 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.1798

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= 0.144
  Angle     :  0.535   7.518   8748  Z= 0.257
  Chirality :  0.036   0.171   1054
  Planarity :  0.003   0.037   1072
  Dihedral  :  3.604  20.247    846
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 14.79 %
    Favored  : 83.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.07 (0.28), residues: 776
  helix:  3.07 (0.18), residues: 660
  sheet:  None (None), residues: 0
  loop :  0.19 (0.60), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 189 
 TYR   0.022   0.001   TYR B 373 
 PHE   0.007   0.001   PHE B 394 
 TRP   0.007   0.001   TRP A  10 
 HIS   0.002   0.001   HIS B  20 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00329 /  0.14 ( 6370)
  covalent geometry    : angle       0.52315 /  0.25 ( 8716)
  SS BOND              : bond        0.00407 /  0.19 (    4)
  SS BOND              : angle       0.96105 /  0.53 (    8)
  hydrogen bonds       : bond        0.04312 /  2.90 (  548)
  hydrogen bonds       : angle       3.53321 /  2.56 ( 1638)
  link_BETA1-4         : bond        0.00247 /  0.13 (    2)
  link_BETA1-4         : angle       1.26608 /  0.63 (    6)
  link_NAG-ASN         : bond        0.00201 /  0.10 (    6)
  link_NAG-ASN         : angle       2.33361 /  1.36 (   18)

*********************** 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
  106 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.136 
Fit side-chains
REVERT: A   35 GLU cc_start: 0.7908 (pm20) cc_final: 0.7456 (pm20)
REVERT: A   56 LEU cc_start: 0.8172 (tt) cc_final: 0.7883 (tp)
REVERT: A   95 LEU cc_start: 0.6833 (OUTLIER) cc_final: 0.6309 (mp)
REVERT: B   22 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.8078 (p0)
REVERT: B  152 GLN cc_start: 0.7607 (mt0) cc_final: 0.7242 (mm-40)
REVERT: B  330 ARG cc_start: 0.7769 (ptm-80) cc_final: 0.7420 (ptp90)
REVERT: B  344 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8520 (mm)
REVERT: B  372 ASP cc_start: 0.7649 (m-30) cc_final: 0.7304 (m-30)
  outliers start: 14
  outliers final: 8
  residues processed: 100
  average time/residue: 0.0931
  time to fit residues: 11.8441
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  : 0.223 
-------------------------------------------------------------------------------
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   44 LEU
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 59 optimal weight:    0.4980
   chunk 45 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 6 optimal weight:    0.3980
   chunk 63 optimal weight:    0.6980
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3383 r_free = 0.3383 target = 0.129588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.107097 restraints weight = 6909.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.3107 rms_B_bonded: 1.54
r_work: 0.2983 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2850 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.1848

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= 0.131
  Angle     :  0.526   7.517   8748  Z= 0.253
  Chirality :  0.036   0.174   1054
  Planarity :  0.003   0.036   1072
  Dihedral  :  3.582  20.039    846
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 14.79 %
    Favored  : 83.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.11 (0.28), residues: 776
  helix:  3.11 (0.18), residues: 660
  sheet:  None (None), residues: 0
  loop :  0.18 (0.60), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 189 
 TYR   0.022   0.001   TYR B 373 
 PHE   0.006   0.001   PHE B 394 
 TRP   0.007   0.001   TRP A  67 
 HIS   0.002   0.001   HIS A 370 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00289 /  0.13 ( 6370)
  covalent geometry    : angle       0.51597 /  0.25 ( 8716)
  SS BOND              : bond        0.00362 /  0.17 (    4)
  SS BOND              : angle       0.90430 /  0.50 (    8)
  hydrogen bonds       : bond        0.04240 /  2.84 (  548)
  hydrogen bonds       : angle       3.49456 /  2.53 ( 1638)
  link_BETA1-4         : bond        0.00274 /  0.14 (    2)
  link_BETA1-4         : angle       1.23621 /  0.61 (    6)
  link_NAG-ASN         : bond        0.00225 /  0.12 (    6)
  link_NAG-ASN         : angle       2.21678 /  1.28 (   18)

********************** 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
  108 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.136 
Fit side-chains
REVERT: A   35 GLU cc_start: 0.7929 (pm20) cc_final: 0.7439 (pm20)
REVERT: A   56 LEU cc_start: 0.8159 (tt) cc_final: 0.7867 (tp)
REVERT: A   95 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6372 (mp)
REVERT: B   22 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7890 (p0)
REVERT: B  127 ARG cc_start: 0.7070 (mmt-90) cc_final: 0.6835 (mmp80)
REVERT: B  166 ARG cc_start: 0.7633 (ttp-110) cc_final: 0.7318 (mtp85)
REVERT: B  330 ARG cc_start: 0.7713 (ptm-80) cc_final: 0.7380 (ptp90)
REVERT: B  344 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8496 (mm)
REVERT: B  372 ASP cc_start: 0.7572 (m-30) cc_final: 0.7304 (m-30)
  outliers start: 14
  outliers final: 8
  residues processed: 102
  average time/residue: 0.0975
  time to fit residues: 12.6671
Evaluate side-chains
  105 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
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   44 LEU
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 55 optimal weight:    0.0040
   chunk 41 optimal weight:    3.9990
   chunk 69 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 58 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   chunk 46 optimal weight:    0.8980
   chunk 31 optimal weight:    5.9990
   chunk 73 optimal weight:    2.9990
   overall best weight:    0.5592

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3386 r_free = 0.3386 target = 0.129872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.107399 restraints weight = 6927.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 1.53
r_work: 0.2985 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2850 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.1889

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     :  0.523   7.514   8748  Z= 0.252
  Chirality :  0.036   0.172   1054
  Planarity :  0.003   0.036   1072
  Dihedral  :  3.567  20.040    846
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.15 (0.29), residues: 776
  helix:  3.14 (0.18), residues: 660
  sheet:  None (None), residues: 0
  loop :  0.18 (0.59), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 330 
 TYR   0.022   0.001   TYR B 373 
 PHE   0.005   0.001   PHE B 394 
 TRP   0.007   0.001   TRP A  67 
 HIS   0.002   0.001   HIS B 370 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00277 /  0.13 ( 6370)
  covalent geometry    : angle       0.51246 /  0.25 ( 8716)
  SS BOND              : bond        0.00375 /  0.18 (    4)
  SS BOND              : angle       0.86860 /  0.48 (    8)
  hydrogen bonds       : bond        0.04198 /  2.81 (  548)
  hydrogen bonds       : angle       3.47261 /  2.51 ( 1638)
  link_BETA1-4         : bond        0.00265 /  0.14 (    2)
  link_BETA1-4         : angle       1.24051 /  0.61 (    6)
  link_NAG-ASN         : bond        0.00233 /  0.12 (    6)
  link_NAG-ASN         : angle       2.18024 /  1.25 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1454.52 seconds
wall clock time: 25 minutes 38.37 seconds (1538.37 seconds total)