Starting phenix.real_space_refine
on Tue Mar  3 14:41:24 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p5c_13198/03_2026/7p5c_13198.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p5c_13198/03_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p5c_13198/03_2026/7p5c_13198.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p5c_13198/03_2026/7p5c_13198.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7p5c_13198/03_2026/7p5c_13198.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p5c_13198/03_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-5986/lib/python3.9/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 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: 1.54, per 1000 atoms: 0.25
  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: 0.62
  Conformation dependent library (CDL) restraints added in 264.8 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: 0.13
  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: 0.82

  Time building geometry restraints manager: 0.81 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: 0.01
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:             0.670
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.400
  Find NCS groups from input model:        0.090
  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:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.660
-------------------------------------------------------------------------------
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 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
  covalent geometry    : bond        0.00435 ( 6370)
  covalent geometry    : angle       0.60434 ( 8716)
  SS BOND              : bond        0.00426 (    4)
  SS BOND              : angle       1.42821 (    8)
  hydrogen bonds       : bond        0.17746 (  548)
  hydrogen bonds       : angle       6.04279 ( 1638)
  link_BETA1-4         : bond        0.00063 (    2)
  link_BETA1-4         : angle       1.62898 (    6)
  link_NAG-ASN         : bond        0.00926 (    6)
  link_NAG-ASN         : angle       2.77095 (   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  : 0.221 
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: 0.0853
  time to fit residues: 11.5954
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  : 0.211 
-------------------------------------------------------------------------------
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...

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 = 0.3368 r_free = 0.3368 target = 0.127968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.105785 restraints weight = 6985.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.3099 rms_B_bonded: 1.53
r_work: 0.2967 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2832 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.1035

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     :  0.602   9.116   8748  Z= 0.292
  Chirality :  0.039   0.222   1054
  Planarity :  0.004   0.035   1072
  Dihedral  :  5.419  50.552   1014
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 5.71
  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:  3.34 (0.29), residues: 776
  helix:  2.62 (0.19), residues: 650
  sheet:  None (None), residues: 0
  loop : -0.05 (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 A  11 
 HIS   0.002   0.001   HIS A 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 6370)
  covalent geometry    : angle       0.58906 ( 8716)
  SS BOND              : bond        0.00382 (    4)
  SS BOND              : angle       1.05151 (    8)
  hydrogen bonds       : bond        0.05108 (  548)
  hydrogen bonds       : angle       4.06013 ( 1638)
  link_BETA1-4         : bond        0.00188 (    2)
  link_BETA1-4         : angle       1.33445 (    6)
  link_NAG-ASN         : bond        0.00730 (    6)
  link_NAG-ASN         : angle       2.67075 (   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  : 0.142 
Fit side-chains
  outliers start: 6
  outliers final: 2
  residues processed: 106
  average time/residue: 0.0784
  time to fit residues: 11.0676
Evaluate side-chains
  94 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 92
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   overall best weight:    0.9182

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.127592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.105294 restraints weight = 6947.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.3089 rms_B_bonded: 1.53
r_work: 0.2960 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2825 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.1317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6382  Z= 0.165
  Angle     :  0.576   8.316   8748  Z= 0.276
  Chirality :  0.038   0.155   1054
  Planarity :  0.003   0.035   1072
  Dihedral  :  4.982  49.363   1014
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  8.08 %
    Favored  : 90.40 %
  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:  3.52 (0.28), residues: 776
  helix:  2.75 (0.18), residues: 650
  sheet:  None (None), residues: 0
  loop : -0.03 (0.56), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 127 
 TYR   0.021   0.001   TYR B 120 
 PHE   0.010   0.001   PHE A 394 
 TRP   0.008   0.001   TRP A  10 
 HIS   0.002   0.001   HIS A 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 6370)
  covalent geometry    : angle       0.55960 ( 8716)
  SS BOND              : bond        0.00433 (    4)
  SS BOND              : angle       1.11115 (    8)
  hydrogen bonds       : bond        0.04771 (  548)
  hydrogen bonds       : angle       3.85001 ( 1638)
  link_BETA1-4         : bond        0.00116 (    2)
  link_BETA1-4         : angle       1.33429 (    6)
  link_NAG-ASN         : bond        0.00530 (    6)
  link_NAG-ASN         : angle       2.88212 (   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
  107 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.217 
Fit side-chains
REVERT: A   56 LEU cc_start: 0.7799 (tt) cc_final: 0.7487 (tp)
REVERT: B   35 GLU cc_start: 0.7591 (tt0) cc_final: 0.7329 (tt0)
  outliers start: 10
  outliers final: 6
  residues processed: 103
  average time/residue: 0.0848
  time to fit residues: 11.4796
Evaluate side-chains
  102 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 96
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 ASP
Chi-restraints excluded: chain B residue   30 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  375 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 29 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 55 optimal weight:    0.6980
   chunk 73 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0770
   chunk 15 optimal weight:    0.8980
   chunk 60 optimal weight:    0.5980
   chunk 76 optimal weight:    0.6980
   overall best weight:    0.5338

-------------------------------------------------------------------------------
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 = 0.3380 r_free = 0.3380 target = 0.129127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.106846 restraints weight = 6943.605|
|-----------------------------------------------------------------------------|
r_work (start): 0.3118 rms_B_bonded: 1.53
r_work: 0.2990 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2854 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.1495

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= 0.131
  Angle     :  0.541   8.009   8748  Z= 0.261
  Chirality :  0.036   0.217   1054
  Planarity :  0.003   0.035   1072
  Dihedral  :  4.579  43.529   1014
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 10.67 %
    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:  3.82 (0.28), residues: 776
  helix:  2.89 (0.18), residues: 662
  sheet:  None (None), residues: 0
  loop :  0.13 (0.61), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 170 
 TYR   0.019   0.001   TYR B 120 
 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
  covalent geometry    : bond        0.00282 ( 6370)
  covalent geometry    : angle       0.52670 ( 8716)
  SS BOND              : bond        0.00358 (    4)
  SS BOND              : angle       0.92533 (    8)
  hydrogen bonds       : bond        0.04412 (  548)
  hydrogen bonds       : angle       3.67350 ( 1638)
  link_BETA1-4         : bond        0.00258 (    2)
  link_BETA1-4         : angle       1.30165 (    6)
  link_NAG-ASN         : bond        0.00329 (    6)
  link_NAG-ASN         : angle       2.65967 (   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
  112 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.238 
Fit side-chains
REVERT: A   35 GLU cc_start: 0.7711 (pm20) cc_final: 0.7406 (pm20)
REVERT: A   56 LEU cc_start: 0.8098 (tt) cc_final: 0.7827 (tp)
REVERT: B   22 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7912 (p0)
REVERT: B   35 GLU cc_start: 0.7724 (tt0) cc_final: 0.7395 (tt0)
REVERT: B  127 ARG cc_start: 0.6837 (mmt180) cc_final: 0.6530 (mmt-90)
  outliers start: 10
  outliers final: 6
  residues processed: 108
  average time/residue: 0.0930
  time to fit residues: 12.9106
Evaluate side-chains
  106 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
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  247 VAL
Chi-restraints excluded: chain B residue  259 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 19 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 2 optimal weight:    0.0770
   chunk 46 optimal weight:    0.5980
   chunk 42 optimal weight:    0.8980
   chunk 62 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.6138

-------------------------------------------------------------------------------
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 = 0.3380 r_free = 0.3380 target = 0.129084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.106725 restraints weight = 7034.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3110 rms_B_bonded: 1.54
r_work: 0.2984 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2849 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.1631

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= 0.133
  Angle     :  0.537   9.419   8748  Z= 0.257
  Chirality :  0.036   0.203   1054
  Planarity :  0.003   0.036   1072
  Dihedral  :  4.255  34.412   1014
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 12.35 %
    Favored  : 85.67 %
  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:  3.97 (0.28), residues: 776
  helix:  3.01 (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   0.006   0.000   ARG A 330 
 TYR   0.020   0.001   TYR B 120 
 PHE   0.006   0.001   PHE B 394 
 TRP   0.007   0.001   TRP A  10 
 HIS   0.002   0.001   HIS A 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 6370)
  covalent geometry    : angle       0.52369 ( 8716)
  SS BOND              : bond        0.00379 (    4)
  SS BOND              : angle       0.91740 (    8)
  hydrogen bonds       : bond        0.04295 (  548)
  hydrogen bonds       : angle       3.56648 ( 1638)
  link_BETA1-4         : bond        0.00325 (    2)
  link_BETA1-4         : angle       1.31889 (    6)
  link_NAG-ASN         : bond        0.00290 (    6)
  link_NAG-ASN         : angle       2.53328 (   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
  116 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A   56 LEU cc_start: 0.8099 (tt) cc_final: 0.7838 (tp)
REVERT: A   95 LEU cc_start: 0.6801 (OUTLIER) cc_final: 0.6333 (mp)
REVERT: B   22 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.8002 (p0)
REVERT: B  127 ARG cc_start: 0.6878 (mmt180) cc_final: 0.6539 (mmt-90)
  outliers start: 13
  outliers final: 9
  residues processed: 110
  average time/residue: 0.0907
  time to fit residues: 12.8431
Evaluate side-chains
  108 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 59 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 9 optimal weight:    0.5980
   chunk 42 optimal weight:    0.8980
   chunk 73 optimal weight:    0.5980
   chunk 52 optimal weight:    4.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3380 r_free = 0.3380 target = 0.129154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.106839 restraints weight = 6888.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3109 rms_B_bonded: 1.51
r_work: 0.2980 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2845 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.1678

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= 0.137
  Angle     :  0.541   8.372   8748  Z= 0.259
  Chirality :  0.036   0.188   1054
  Planarity :  0.003   0.036   1072
  Dihedral  :  4.047  24.658   1014
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 13.11 %
    Favored  : 84.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  4.01 (0.28), residues: 776
  helix:  3.04 (0.18), residues: 660
  sheet:  None (None), residues: 0
  loop :  0.13 (0.59), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 330 
 TYR   0.021   0.001   TYR B 373 
 PHE   0.006   0.001   PHE B 394 
 TRP   0.007   0.001   TRP A  10 
 HIS   0.002   0.001   HIS A 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 6370)
  covalent geometry    : angle       0.52875 ( 8716)
  SS BOND              : bond        0.00389 (    4)
  SS BOND              : angle       0.92668 (    8)
  hydrogen bonds       : bond        0.04290 (  548)
  hydrogen bonds       : angle       3.54267 ( 1638)
  link_BETA1-4         : bond        0.00208 (    2)
  link_BETA1-4         : angle       1.30576 (    6)
  link_NAG-ASN         : bond        0.00206 (    6)
  link_NAG-ASN         : angle       2.42562 (   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
  111 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.219 
Fit side-chains
REVERT: A   35 GLU cc_start: 0.7771 (pm20) cc_final: 0.7407 (pm20)
REVERT: A   56 LEU cc_start: 0.8105 (tt) cc_final: 0.7810 (tp)
REVERT: A   95 LEU cc_start: 0.6730 (OUTLIER) cc_final: 0.6237 (mp)
REVERT: A  327 GLU cc_start: 0.8069 (tp30) cc_final: 0.7861 (mm-30)
REVERT: B   22 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7948 (p0)
REVERT: B  127 ARG cc_start: 0.6776 (mmt180) cc_final: 0.6414 (mmt-90)
  outliers start: 14
  outliers final: 10
  residues processed: 105
  average time/residue: 0.0988
  time to fit residues: 13.2512
Evaluate side-chains
  109 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 31 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 70 optimal weight:    0.4980
   chunk 10 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0970
   chunk 66 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 75 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   overall best weight:    0.5978

-------------------------------------------------------------------------------
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 = 0.3384 r_free = 0.3384 target = 0.129574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.107184 restraints weight = 6916.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 1.54
r_work: 0.2989 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2854 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.1762

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= 0.128
  Angle     :  0.528   8.181   8748  Z= 0.253
  Chirality :  0.036   0.178   1054
  Planarity :  0.003   0.036   1072
  Dihedral  :  3.894  22.232   1014
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 13.26 %
    Favored  : 84.30 %
  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:  4.10 (0.28), residues: 776
  helix:  3.10 (0.18), residues: 660
  sheet:  None (None), residues: 0
  loop :  0.17 (0.59), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 330 
 TYR   0.020   0.001   TYR B 373 
 PHE   0.005   0.001   PHE B 394 
 TRP   0.007   0.001   TRP A  10 
 HIS   0.002   0.001   HIS A 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 6370)
  covalent geometry    : angle       0.51634 ( 8716)
  SS BOND              : bond        0.00358 (    4)
  SS BOND              : angle       0.88382 (    8)
  hydrogen bonds       : bond        0.04221 (  548)
  hydrogen bonds       : angle       3.48693 ( 1638)
  link_BETA1-4         : bond        0.00220 (    2)
  link_BETA1-4         : angle       1.30306 (    6)
  link_NAG-ASN         : bond        0.00222 (    6)
  link_NAG-ASN         : angle       2.31185 (   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
  121 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.235 
Fit side-chains
REVERT: A   35 GLU cc_start: 0.7812 (pm20) cc_final: 0.7416 (pm20)
REVERT: A   56 LEU cc_start: 0.8108 (tt) cc_final: 0.7818 (tp)
REVERT: A   95 LEU cc_start: 0.6787 (OUTLIER) cc_final: 0.6332 (mp)
REVERT: B   22 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7896 (p0)
REVERT: B  127 ARG cc_start: 0.6683 (mmt180) cc_final: 0.6340 (mmt-90)
REVERT: B  152 GLN cc_start: 0.7536 (mt0) cc_final: 0.7200 (mm-40)
REVERT: B  330 ARG cc_start: 0.7734 (ptm-80) cc_final: 0.7365 (ptp90)
REVERT: B  390 TYR cc_start: 0.8578 (m-80) cc_final: 0.8356 (m-10)
  outliers start: 16
  outliers final: 11
  residues processed: 114
  average time/residue: 0.1064
  time to fit residues: 15.4085
Evaluate side-chains
  113 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
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  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  375 GLN
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:    0.8980
   chunk 69 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   chunk 52 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   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**

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 = 0.128431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.106123 restraints weight = 6968.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.3111 rms_B_bonded: 1.53
r_work: 0.2986 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.2852 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.1760

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     :  0.549   7.930   8748  Z= 0.262
  Chirality :  0.037   0.170   1054
  Planarity :  0.003   0.037   1072
  Dihedral  :  3.930  22.697   1014
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 15.09 %
    Favored  : 82.62 %
  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:  4.01 (0.29), residues: 776
  helix:  3.03 (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   0.004   0.000   ARG A 330 
 TYR   0.023   0.001   TYR B 373 
 PHE   0.008   0.001   PHE B 394 
 TRP   0.007   0.001   TRP A  10 
 HIS   0.002   0.001   HIS A 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 6370)
  covalent geometry    : angle       0.53748 ( 8716)
  SS BOND              : bond        0.00440 (    4)
  SS BOND              : angle       0.97746 (    8)
  hydrogen bonds       : bond        0.04348 (  548)
  hydrogen bonds       : angle       3.54729 ( 1638)
  link_BETA1-4         : bond        0.00172 (    2)
  link_BETA1-4         : angle       1.41910 (    6)
  link_NAG-ASN         : bond        0.00178 (    6)
  link_NAG-ASN         : angle       2.37183 (   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
  113 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.243 
Fit side-chains
REVERT: A   35 GLU cc_start: 0.7961 (pm20) cc_final: 0.7476 (pm20)
REVERT: A   56 LEU cc_start: 0.8163 (tt) cc_final: 0.7874 (tp)
REVERT: A   95 LEU cc_start: 0.6836 (OUTLIER) cc_final: 0.6312 (mp)
REVERT: B   22 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7931 (p0)
REVERT: B  152 GLN cc_start: 0.7596 (mt0) cc_final: 0.7228 (mm-40)
REVERT: B  330 ARG cc_start: 0.7721 (ptm-80) cc_final: 0.7375 (ptp90)
  outliers start: 15
  outliers final: 9
  residues processed: 107
  average time/residue: 0.0992
  time to fit residues: 13.5462
Evaluate side-chains
  108 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
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
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:    1.9990
   chunk 52 optimal weight:    5.9990
   chunk 50 optimal weight:    3.9990
   chunk 47 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0170
   chunk 51 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9990
   chunk 54 optimal weight:    0.7980
   overall best weight:    0.6218

-------------------------------------------------------------------------------
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 = 0.3378 r_free = 0.3378 target = 0.129184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.106876 restraints weight = 6990.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.3102 rms_B_bonded: 1.54
r_work: 0.2974 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2839 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.1806

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     :  0.537   7.882   8748  Z= 0.256
  Chirality :  0.036   0.179   1054
  Planarity :  0.003   0.036   1072
  Dihedral  :  3.863  22.905   1014
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 15.24 %
    Favored  : 82.62 %
  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 (0.29), residues: 776
  helix:  3.09 (0.18), residues: 660
  sheet:  None (None), residues: 0
  loop :  0.17 (0.59), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 330 
 TYR   0.022   0.001   TYR B 373 
 PHE   0.006   0.001   PHE B 394 
 TRP   0.007   0.001   TRP A  10 
 HIS   0.001   0.001   HIS B  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 6370)
  covalent geometry    : angle       0.52564 ( 8716)
  SS BOND              : bond        0.00368 (    4)
  SS BOND              : angle       0.89522 (    8)
  hydrogen bonds       : bond        0.04266 (  548)
  hydrogen bonds       : angle       3.50404 ( 1638)
  link_BETA1-4         : bond        0.00240 (    2)
  link_BETA1-4         : angle       1.39885 (    6)
  link_NAG-ASN         : bond        0.00204 (    6)
  link_NAG-ASN         : angle       2.28656 (   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
  111 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A   35 GLU cc_start: 0.7908 (pm20) cc_final: 0.7439 (pm20)
REVERT: A   56 LEU cc_start: 0.8117 (tt) cc_final: 0.7826 (tp)
REVERT: A   95 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.6324 (mp)
REVERT: B   22 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7889 (p0)
REVERT: B  166 ARG cc_start: 0.7601 (ttp-110) cc_final: 0.7288 (mtp85)
REVERT: B  330 ARG cc_start: 0.7676 (ptm-80) cc_final: 0.7347 (ptp90)
  outliers start: 14
  outliers final: 10
  residues processed: 105
  average time/residue: 0.1000
  time to fit residues: 13.3195
Evaluate side-chains
  109 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   44 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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 36 optimal weight:    0.8980
   chunk 46 optimal weight:    0.8980
   chunk 59 optimal weight:    0.5980
   chunk 45 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 6 optimal weight:    0.4980
   chunk 63 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3378 r_free = 0.3378 target = 0.129288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.106906 restraints weight = 6910.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.3113 rms_B_bonded: 1.54
r_work: 0.2988 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2855 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.2855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.1821

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= 0.134
  Angle     :  0.543   8.081   8748  Z= 0.258
  Chirality :  0.036   0.176   1054
  Planarity :  0.003   0.037   1072
  Dihedral  :  3.856  22.971   1014
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 15.55 %
    Favored  : 82.62 %
  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:  4.06 (0.29), residues: 776
  helix:  3.07 (0.18), residues: 660
  sheet:  None (None), residues: 0
  loop :  0.16 (0.59), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 330 
 TYR   0.021   0.001   TYR B 373 
 PHE   0.006   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
  covalent geometry    : bond        0.00300 ( 6370)
  covalent geometry    : angle       0.53257 ( 8716)
  SS BOND              : bond        0.00383 (    4)
  SS BOND              : angle       0.91880 (    8)
  hydrogen bonds       : bond        0.04271 (  548)
  hydrogen bonds       : angle       3.50543 ( 1638)
  link_BETA1-4         : bond        0.00186 (    2)
  link_BETA1-4         : angle       1.41843 (    6)
  link_NAG-ASN         : bond        0.00196 (    6)
  link_NAG-ASN         : angle       2.26733 (   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
  110 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.219 
Fit side-chains
REVERT: A   35 GLU cc_start: 0.7851 (pm20) cc_final: 0.7431 (pm20)
REVERT: A   56 LEU cc_start: 0.8200 (tt) cc_final: 0.7909 (tp)
REVERT: A   95 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6443 (mp)
REVERT: A  327 GLU cc_start: 0.8100 (tp30) cc_final: 0.7814 (mm-30)
REVERT: B   22 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7914 (p0)
REVERT: B  127 ARG cc_start: 0.7142 (mmt-90) cc_final: 0.6906 (mmp80)
REVERT: B  166 ARG cc_start: 0.7594 (ttp-110) cc_final: 0.7346 (mtp85)
REVERT: B  330 ARG cc_start: 0.7715 (ptm-80) cc_final: 0.7419 (ptp90)
REVERT: B  372 ASP cc_start: 0.7679 (m-30) cc_final: 0.7362 (m-30)
  outliers start: 12
  outliers final: 10
  residues processed: 106
  average time/residue: 0.1029
  time to fit residues: 13.7311
Evaluate side-chains
  108 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   44 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  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  375 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 55 optimal weight:    0.0770
   chunk 41 optimal weight:    5.9990
   chunk 69 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 1 optimal weight:    0.3980
   chunk 7 optimal weight:    0.9990
   chunk 58 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   chunk 31 optimal weight:    4.9990
   chunk 73 optimal weight:    2.9990
   overall best weight:    0.5338

-------------------------------------------------------------------------------
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 = 0.3384 r_free = 0.3384 target = 0.129890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.107461 restraints weight = 6901.519|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 1.53
r_work: 0.2982 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2846 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.2846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.1842

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= 0.125
  Angle     :  0.536   7.858   8748  Z= 0.255
  Chirality :  0.036   0.179   1054
  Planarity :  0.003   0.036   1072
  Dihedral  :  3.817  22.607   1014
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 15.40 %
    Favored  : 82.47 %
  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 (0.29), residues: 776
  helix:  3.09 (0.19), residues: 662
  sheet:  None (None), residues: 0
  loop :  0.23 (0.60), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 330 
 TYR   0.023   0.001   TYR B 373 
 PHE   0.005   0.001   PHE B 394 
 TRP   0.007   0.001   TRP A  10 
 HIS   0.001   0.001   HIS A 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 6370)
  covalent geometry    : angle       0.52565 ( 8716)
  SS BOND              : bond        0.00355 (    4)
  SS BOND              : angle       0.88862 (    8)
  hydrogen bonds       : bond        0.04223 (  548)
  hydrogen bonds       : angle       3.48019 ( 1638)
  link_BETA1-4         : bond        0.00205 (    2)
  link_BETA1-4         : angle       1.42209 (    6)
  link_NAG-ASN         : bond        0.00212 (    6)
  link_NAG-ASN         : angle       2.23779 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1496.70 seconds
wall clock time: 26 minutes 17.85 seconds (1577.85 seconds total)