Starting phenix.real_space_refine
on Thu Jul 24 13:33:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p5j_13200/07_2025/7p5j_13200.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p5j_13200/07_2025/7p5j_13200.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7p5j_13200/07_2025/7p5j_13200.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p5j_13200/07_2025/7p5j_13200.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p5j_13200/07_2025/7p5j_13200.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p5j_13200/07_2025/7p5j_13200.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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      24      5.16       5
     C    4034      2.51       5
     N    1036      2.21       5
     O    1156      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6250
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3069
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 399, 3069
          Classifications: {'peptide': 399}
          Link IDs: {'PTRANS': 17, 'TRANS': 381}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3069
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 399, 3069
          Classifications: {'peptide': 399}
          Link IDs: {'PTRANS': 17, 'TRANS': 381}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 4.36, per 1000 atoms: 0.70
  Number of scatterers: 6250
  At special positions: 0
  Unit cell: (88.536, 71.61, 134.106, 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      24     16.00
     O    1156      8.00
     N    1036      7.00
     C    4034      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 275 " - pdb=" SG  CYS A 385 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 303 " - pdb=" SG  CYS A 370 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 275 " - pdb=" SG  CYS B 385 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 303 " - pdb=" SG  CYS B 370 " 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 501 " - " ASN A 284 "
      " NAG A 502 " - " ASN A 355 "
      " NAG B 501 " - " ASN B 284 "
      " NAG B 502 " - " ASN B 355 "
      " NAG C   1 " - " ASN A 130 "
      " NAG D   1 " - " ASN B 130 "
  Time building additional restraints: 1.58
  Conformation dependent library (CDL) restraints added in 937.1 milliseconds
  

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1496

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 0 sheets defined
      86.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 18
      removed outlier: 3.604A  pdb=" N   HIS A  14 " --> pdb=" O   SER A  10 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 70
      removed outlier: 3.591A  pdb=" N   GLN A  41 " --> pdb=" O   GLU A  37 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   VAL A  47 " --> pdb=" O   ALA A  43 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ALA A  48 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 161
    Processing helix  chain 'A' and resid 167 through 187
    Processing helix  chain 'A' and resid 198 through 238
      removed outlier: 3.636A  pdb=" N   VAL A 202 " --> pdb=" O   SER A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 239 through 276
      removed outlier: 4.116A  pdb=" N   VAL A 248 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   MET A 249 " --> pdb=" O   VAL A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 290
    Processing helix  chain 'A' and resid 293 through 303
      removed outlier: 3.755A  pdb=" N   LEU A 297 " --> pdb=" O   SER A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 335
      removed outlier: 3.759A  pdb=" N   ARG A 320 " --> pdb=" O   THR A 316 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   GLN A 328 " --> pdb=" O   ASN A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 340
      removed outlier: 3.805A  pdb=" N   GLN A 339 " --> pdb=" O   GLU A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 368
      removed outlier: 3.565A  pdb=" N   LYS A 345 " --> pdb=" O   PRO A 341 " (cutoff:3.500A)
      Proline residue:  A 346  - end of helix
      removed outlier: 4.183A  pdb=" N   SER A 349 " --> pdb=" O   LYS A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 386
      removed outlier: 4.266A  pdb=" N   LEU A 373 " --> pdb=" O   HIS A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 418
      Proline residue:  A 414  - end of helix
      removed outlier: 4.580A  pdb=" N   ALA A 418 " --> pdb=" O   PRO A 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 18
    Processing helix  chain 'B' and resid 37 through 70
      removed outlier: 3.620A  pdb=" N   ALA B  48 " --> pdb=" O   LEU B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 91 through 161
    Processing helix  chain 'B' and resid 167 through 190
      removed outlier: 3.694A  pdb=" N   ALA B 190 " --> pdb=" O   LEU B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 198 through 238
      removed outlier: 3.757A  pdb=" N   VAL B 202 " --> pdb=" O   SER B 198 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ASN B 205 " --> pdb=" O   GLN B 201 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   VAL B 206 " --> pdb=" O   VAL B 202 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 239 through 275
      removed outlier: 4.010A  pdb=" N   VAL B 248 " --> pdb=" O   ILE B 244 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   MET B 249 " --> pdb=" O   VAL B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 290
    Processing helix  chain 'B' and resid 293 through 303
    Processing helix  chain 'B' and resid 311 through 335
    Processing helix  chain 'B' and resid 335 through 340
      removed outlier: 3.925A  pdb=" N   GLN B 339 " --> pdb=" O   GLU B 335 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 343 through 368
    Processing helix  chain 'B' and resid 369 through 385
      removed outlier: 4.120A  pdb=" N   LEU B 373 " --> pdb=" O   HIS B 369 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   LYS B 375 " --> pdb=" O   ARG B 371 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   ASP B 376 " --> pdb=" O   SER B 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 418
      Proline residue:  B 414  - end of helix
      removed outlier: 4.576A  pdb=" N   ALA B 418 " --> pdb=" O   PRO B 414 " (cutoff:3.500A)

    552 hydrogen bonds defined for protein.
    1656 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: 1.69

  Time building geometry restraints manager: 1.88 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: 1975
        1.34 -     1.46: 1103
        1.46 -     1.58: 3270
        1.58 -     1.70: 0
        1.70 -     1.82: 30
  Bond restraints: 6378
  Sorted by residual:
  bond pdb=" N   ILE B 244 "
       pdb=" CA  ILE B 244 "
    ideal  model  delta    sigma   weight residual
    1.461  1.499 -0.038 1.19e-02 7.06e+03 1.03e+01
  bond pdb=" CA  PRO A 421 "
       pdb=" C   PRO A 421 "
    ideal  model  delta    sigma   weight residual
    1.517  1.545 -0.028 9.30e-03 1.16e+04 9.10e+00
  bond pdb=" N   VAL B 243 "
       pdb=" CA  VAL B 243 "
    ideal  model  delta    sigma   weight residual
    1.463  1.495 -0.032 1.14e-02 7.69e+03 8.03e+00
  bond pdb=" N   ASP B 137 "
       pdb=" CA  ASP B 137 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.25e-02 6.40e+03 7.79e+00
  bond pdb=" N   LEU B 242 "
       pdb=" CA  LEU B 242 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.16e-02 7.43e+03 6.65e+00
  ... (remaining 6373 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.50: 8296
        1.50 -     3.00: 297
        3.00 -     4.50: 77
        4.50 -     6.00: 29
        6.00 -     7.51: 5
  Bond angle restraints: 8704
  Sorted by residual:
  angle pdb=" N   PRO A 421 "
        pdb=" CA  PRO A 421 "
        pdb=" C   PRO A 421 "
      ideal   model   delta    sigma   weight residual
     110.70  116.89   -6.19 1.22e+00 6.72e-01 2.57e+01
  angle pdb=" CA  PRO B 421 "
        pdb=" C   PRO B 421 "
        pdb=" N   PRO B 422 "
      ideal   model   delta    sigma   weight residual
     117.93  123.81   -5.88 1.20e+00 6.94e-01 2.40e+01
  angle pdb=" CA  PRO A 421 "
        pdb=" C   PRO A 421 "
        pdb=" N   PRO A 422 "
      ideal   model   delta    sigma   weight residual
     117.93  123.57   -5.64 1.20e+00 6.94e-01 2.21e+01
  angle pdb=" O   PRO B 421 "
        pdb=" C   PRO B 421 "
        pdb=" N   PRO B 422 "
      ideal   model   delta    sigma   weight residual
     121.46  116.44    5.02 1.18e+00 7.18e-01 1.81e+01
  angle pdb=" CA  ASP B 137 "
        pdb=" CB  ASP B 137 "
        pdb=" CG  ASP B 137 "
      ideal   model   delta    sigma   weight residual
     112.60  116.68   -4.08 1.00e+00 1.00e+00 1.67e+01
  ... (remaining 8699 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.06: 3516
       21.06 -    42.12: 296
       42.12 -    63.18: 58
       63.18 -    84.24: 15
       84.24 -   105.30: 15
  Dihedral angle restraints: 3900
    sinusoidal: 1590
      harmonic: 2310
  Sorted by residual:
  dihedral pdb=" CB  CYS B 303 "
           pdb=" SG  CYS B 303 "
           pdb=" SG  CYS B 370 "
           pdb=" CB  CYS B 370 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00    9.23   83.77     1      1.00e+01 1.00e-02 8.56e+01
  dihedral pdb=" CA  ASP B 279 "
           pdb=" C   ASP B 279 "
           pdb=" N   PRO B 280 "
           pdb=" CA  PRO B 280 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.22   18.78     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" C2  NAG C   2 "
           pdb=" C3  NAG C   2 "
           pdb=" C4  NAG C   2 "
           pdb=" O4  NAG C   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     175.11   69.81  105.30     1      3.00e+01 1.11e-03 1.35e+01
  ... (remaining 3897 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 930
       0.061 -    0.122: 131
       0.122 -    0.182: 8
       0.182 -    0.243: 2
       0.243 -    0.304: 1
  Chirality restraints: 1072
  Sorted by residual:
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.16   -0.24 2.00e-02 2.50e+03 1.39e+02
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN A 130 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.10   -0.30 2.00e-01 2.50e+01 2.31e+00
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN B 130 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.16   -0.24 2.00e-01 2.50e+01 1.44e+00
  ... (remaining 1069 not shown)

  Planarity restraints: 1092
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   2 "    0.295 2.00e-02 2.50e+03   2.56e-01 8.19e+02
        pdb=" C7  NAG D   2 "   -0.067 2.00e-02 2.50e+03
        pdb=" C8  NAG D   2 "    0.158 2.00e-02 2.50e+03
        pdb=" N2  NAG D   2 "   -0.454 2.00e-02 2.50e+03
        pdb=" O7  NAG D   2 "    0.068 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   1 "   -0.266 2.00e-02 2.50e+03   2.21e-01 6.13e+02
        pdb=" C7  NAG D   1 "    0.073 2.00e-02 2.50e+03
        pdb=" C8  NAG D   1 "   -0.183 2.00e-02 2.50e+03
        pdb=" N2  NAG D   1 "    0.368 2.00e-02 2.50e+03
        pdb=" O7  NAG D   1 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 130 "   -0.025 2.00e-02 2.50e+03   2.36e-02 6.95e+00
        pdb=" CG  ASN A 130 "    0.036 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 130 "   -0.007 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 130 "    0.018 2.00e-02 2.50e+03
        pdb=" C1  NAG C   1 "   -0.022 2.00e-02 2.50e+03
  ... (remaining 1089 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1361
        2.79 -     3.32: 6914
        3.32 -     3.85: 10669
        3.85 -     4.37: 11531
        4.37 -     4.90: 19376
  Nonbonded interactions: 49851
  Sorted by model distance:
  nonbonded pdb=" O   GLU B 154 "
            pdb=" OG1 THR B 157 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" O   GLU A 154 "
            pdb=" OG1 THR A 157 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" O   VAL A  90 "
            pdb=" OG  SER A  93 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" O3  NAG C   1 "
            pdb=" O7  NAG C   2 "
     model   vdw
     2.330 3.040
  nonbonded pdb=" OD1 ASN A 205 "
            pdb=" N   VAL A 206 "
     model   vdw
     2.344 3.120
  ... (remaining 49846 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.180
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.440
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
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   0.051   6390  Z= 0.242
  Angle     :  0.743   8.578   8736  Z= 0.408
  Chirality :  0.043   0.304   1072
  Planarity :  0.011   0.256   1086
  Dihedral  : 17.475 105.301   2392
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  1.51 %
    Favored  : 97.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.65 (0.31), residues: 790
  helix:  2.36 (0.20), residues: 658
  sheet:  None (None), residues: 0
  loop : -1.51 (0.54), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 258 
 HIS   0.004   0.001   HIS B 128 
 PHE   0.029   0.002   PHE B 208 
 TYR   0.026   0.002   TYR A 299 
 ARG   0.004   0.000   ARG A 314 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01937 (    6)
  link_NAG-ASN         : angle       2.57245 (   18)
  link_BETA1-4         : bond        0.02207 (    2)
  link_BETA1-4         : angle       4.68117 (    6)
  hydrogen bonds       : bond        0.10764 (  552)
  hydrogen bonds       : angle       5.18823 ( 1656)
  SS BOND              : bond        0.00192 (    4)
  SS BOND              : angle       0.65457 (    8)
  covalent geometry    : bond        0.00402 ( 6378)
  covalent geometry    : angle       0.72498 ( 8704)

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

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 239
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
REVERT: A  273 ASP cc_start: 0.7622 (t70) cc_final: 0.6956 (t70)
REVERT: A  350 LEU cc_start: 0.8933 (mt) cc_final: 0.8660 (mt)
REVERT: B   40 TYR cc_start: 0.7595 (t80) cc_final: 0.7385 (t80)
REVERT: B   98 LEU cc_start: 0.8265 (mm) cc_final: 0.8063 (mm)
REVERT: B  134 SER cc_start: 0.8916 (m) cc_final: 0.8442 (t)
REVERT: B  160 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8679 (tm-30)
REVERT: B  167 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7288 (tp30)
REVERT: B  304 ASN cc_start: 0.8119 (m-40) cc_final: 0.7634 (m-40)
  outliers start: 4
  outliers final: 2
  residues processed: 241
  average time/residue: 0.1733
  time to fit residues: 57.9993
Evaluate side-chains
  204 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 202
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  240 LYS
Chi-restraints excluded: chain B residue  244 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 59 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 39 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 70 optimal weight:   10.0000
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
B 128 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.153476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.132391 restraints weight = 9925.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.135709 restraints weight = 5993.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.137867 restraints weight = 4159.245|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.1557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6390  Z= 0.190
  Angle     :  0.746   9.467   8736  Z= 0.347
  Chirality :  0.045   0.216   1072
  Planarity :  0.005   0.069   1086
  Dihedral  : 10.270  73.404   1024
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 16.01 %
    Favored  : 81.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.00 (0.30), residues: 790
  helix:  2.55 (0.20), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.31 (0.57), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 258 
 HIS   0.006   0.001   HIS B  17 
 PHE   0.034   0.002   PHE A 208 
 TYR   0.021   0.002   TYR A 377 
 ARG   0.003   0.000   ARG B 173 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00311 (    6)
  link_NAG-ASN         : angle       1.34198 (   18)
  link_BETA1-4         : bond        0.01413 (    2)
  link_BETA1-4         : angle       4.04519 (    6)
  hydrogen bonds       : bond        0.04379 (  552)
  hydrogen bonds       : angle       4.29771 ( 1656)
  SS BOND              : bond        0.00652 (    4)
  SS BOND              : angle       1.20608 (    8)
  covalent geometry    : bond        0.00408 ( 6378)
  covalent geometry    : angle       0.73647 ( 8704)

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

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 219
  time to evaluate  : 0.720 
Fit side-chains
REVERT: A   40 TYR cc_start: 0.7956 (t80) cc_final: 0.7743 (t80)
REVERT: A  131 HIS cc_start: 0.8144 (t70) cc_final: 0.7893 (t70)
REVERT: A  273 ASP cc_start: 0.7523 (t70) cc_final: 0.7158 (t70)
REVERT: A  381 LEU cc_start: 0.8650 (mt) cc_final: 0.8428 (mt)
REVERT: B  134 SER cc_start: 0.9013 (m) cc_final: 0.8155 (t)
REVERT: B  304 ASN cc_start: 0.8257 (m-40) cc_final: 0.7738 (m-40)
  outliers start: 16
  outliers final: 11
  residues processed: 224
  average time/residue: 0.1496
  time to fit residues: 46.2065
Evaluate side-chains
  216 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 205
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 CYS
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  134 SER
Chi-restraints excluded: chain A residue  159 GLU
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  279 ASP
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  347 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 64 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   chunk 53 optimal weight:    0.4980
   chunk 22 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 73 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 128 HIS
B 324 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.156144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.134885 restraints weight = 10049.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.138375 restraints weight = 6093.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.140839 restraints weight = 4192.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.1824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6390  Z= 0.145
  Angle     :  0.703  10.265   8736  Z= 0.325
  Chirality :  0.041   0.180   1072
  Planarity :  0.005   0.062   1086
  Dihedral  :  8.040  57.530   1018
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 17.82 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.16 (0.30), residues: 790
  helix:  2.67 (0.20), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.36 (0.58), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 258 
 HIS   0.005   0.001   HIS B 326 
 PHE   0.036   0.002   PHE B 208 
 TYR   0.027   0.002   TYR A 299 
 ARG   0.002   0.000   ARG A 314 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00479 (    6)
  link_NAG-ASN         : angle       1.18594 (   18)
  link_BETA1-4         : bond        0.02200 (    2)
  link_BETA1-4         : angle       3.96425 (    6)
  hydrogen bonds       : bond        0.04073 (  552)
  hydrogen bonds       : angle       4.12167 ( 1656)
  SS BOND              : bond        0.00772 (    4)
  SS BOND              : angle       1.04348 (    8)
  covalent geometry    : bond        0.00306 ( 6378)
  covalent geometry    : angle       0.69325 ( 8704)

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

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 212
  time to evaluate  : 0.679 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 TYR cc_start: 0.7919 (t80) cc_final: 0.7663 (t80)
REVERT: A  273 ASP cc_start: 0.7677 (t70) cc_final: 0.7198 (t70)
REVERT: A  381 LEU cc_start: 0.8705 (mt) cc_final: 0.8327 (mt)
REVERT: A  402 SER cc_start: 0.8753 (p) cc_final: 0.8222 (t)
REVERT: B  134 SER cc_start: 0.9001 (m) cc_final: 0.8188 (t)
REVERT: B  214 TRP cc_start: 0.6928 (t60) cc_final: 0.6488 (t60)
REVERT: B  240 LYS cc_start: 0.7600 (mttp) cc_final: 0.7272 (mttp)
REVERT: B  304 ASN cc_start: 0.8202 (m-40) cc_final: 0.7773 (m-40)
REVERT: B  381 LEU cc_start: 0.8593 (mt) cc_final: 0.8214 (mt)
REVERT: B  402 SER cc_start: 0.8686 (p) cc_final: 0.8186 (t)
  outliers start: 17
  outliers final: 13
  residues processed: 220
  average time/residue: 0.1415
  time to fit residues: 43.2000
Evaluate side-chains
  213 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 200
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue   94 CYS
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  159 GLU
Chi-restraints excluded: chain A residue  211 GLU
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  350 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 64 optimal weight:    0.4980
   chunk 77 optimal weight:    5.9990
   chunk 63 optimal weight:    0.6980
   chunk 36 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 70 optimal weight:    0.0170
   chunk 71 optimal weight:    0.9980
   chunk 68 optimal weight:    0.6980
   chunk 52 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:
B 128 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.156891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.135757 restraints weight = 10246.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.139359 restraints weight = 6075.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.141791 restraints weight = 4142.318|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.2053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6390  Z= 0.139
  Angle     :  0.702  11.074   8736  Z= 0.320
  Chirality :  0.040   0.216   1072
  Planarity :  0.005   0.060   1086
  Dihedral  :  7.058  55.907   1018
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 19.64 %
    Favored  : 77.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.24 (0.30), residues: 790
  helix:  2.75 (0.20), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.44 (0.55), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 258 
 HIS   0.005   0.001   HIS B 326 
 PHE   0.028   0.002   PHE B 208 
 TYR   0.017   0.002   TYR A 299 
 ARG   0.001   0.000   ARG A 213 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00494 (    6)
  link_NAG-ASN         : angle       1.16563 (   18)
  link_BETA1-4         : bond        0.02220 (    2)
  link_BETA1-4         : angle       4.24639 (    6)
  hydrogen bonds       : bond        0.03845 (  552)
  hydrogen bonds       : angle       4.00733 ( 1656)
  SS BOND              : bond        0.01024 (    4)
  SS BOND              : angle       1.27854 (    8)
  covalent geometry    : bond        0.00297 ( 6378)
  covalent geometry    : angle       0.69139 ( 8704)

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

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 211
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 TYR cc_start: 0.7959 (t80) cc_final: 0.7722 (t80)
REVERT: A  273 ASP cc_start: 0.7631 (t70) cc_final: 0.7130 (t70)
REVERT: A  381 LEU cc_start: 0.8653 (mt) cc_final: 0.8305 (mt)
REVERT: A  402 SER cc_start: 0.8692 (p) cc_final: 0.8164 (t)
REVERT: B  134 SER cc_start: 0.8990 (m) cc_final: 0.8111 (t)
REVERT: B  214 TRP cc_start: 0.6744 (t60) cc_final: 0.6462 (t60)
REVERT: B  240 LYS cc_start: 0.7548 (mttp) cc_final: 0.7245 (mttp)
REVERT: B  304 ASN cc_start: 0.8241 (m-40) cc_final: 0.7899 (m-40)
REVERT: B  381 LEU cc_start: 0.8597 (mt) cc_final: 0.8061 (mt)
REVERT: B  402 SER cc_start: 0.8665 (p) cc_final: 0.8165 (t)
  outliers start: 22
  outliers final: 16
  residues processed: 219
  average time/residue: 0.1504
  time to fit residues: 45.0069
Evaluate side-chains
  218 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 202
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue   94 CYS
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  159 GLU
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  240 LYS
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  142 GLU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  350 LEU
Chi-restraints excluded: chain B residue  358 GLU
Chi-restraints excluded: chain B residue  392 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 75 optimal weight:    0.2980
   chunk 77 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 53 optimal weight:    0.5980
   chunk 43 optimal weight:    4.9990
   chunk 6 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9990
   chunk 40 optimal weight:    6.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 138 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.155752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.134758 restraints weight = 10205.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.138244 restraints weight = 6072.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.140770 restraints weight = 4157.353|
|-----------------------------------------------------------------------------|
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.2237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   6390  Z= 0.145
  Angle     :  0.722  13.936   8736  Z= 0.326
  Chirality :  0.040   0.167   1072
  Planarity :  0.005   0.056   1086
  Dihedral  :  6.722  59.348   1018
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 21.15 %
    Favored  : 75.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.24 (0.30), residues: 790
  helix:  2.79 (0.19), residues: 662
  sheet:  None (None), residues: 0
  loop : -1.59 (0.53), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 258 
 HIS   0.009   0.001   HIS B 138 
 PHE   0.016   0.001   PHE B 208 
 TYR   0.017   0.002   TYR A 299 
 ARG   0.002   0.000   ARG A 146 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00453 (    6)
  link_NAG-ASN         : angle       1.23439 (   18)
  link_BETA1-4         : bond        0.02025 (    2)
  link_BETA1-4         : angle       4.28384 (    6)
  hydrogen bonds       : bond        0.03781 (  552)
  hydrogen bonds       : angle       3.98789 ( 1656)
  SS BOND              : bond        0.00302 (    4)
  SS BOND              : angle       1.36468 (    8)
  covalent geometry    : bond        0.00321 ( 6378)
  covalent geometry    : angle       0.71089 ( 8704)

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

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 212
  time to evaluate  : 0.631 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 TYR cc_start: 0.8087 (t80) cc_final: 0.7735 (t80)
REVERT: A  273 ASP cc_start: 0.7689 (t70) cc_final: 0.7128 (t70)
REVERT: A  381 LEU cc_start: 0.8562 (mt) cc_final: 0.8078 (mt)
REVERT: A  402 SER cc_start: 0.8646 (p) cc_final: 0.8091 (t)
REVERT: B  134 SER cc_start: 0.9041 (m) cc_final: 0.8165 (t)
REVERT: B  240 LYS cc_start: 0.7546 (mttp) cc_final: 0.7275 (mttp)
REVERT: B  246 MET cc_start: 0.7464 (ppp) cc_final: 0.6165 (ppp)
REVERT: B  304 ASN cc_start: 0.8246 (m-40) cc_final: 0.7830 (m-40)
REVERT: B  381 LEU cc_start: 0.8705 (mt) cc_final: 0.8033 (mt)
REVERT: B  402 SER cc_start: 0.8643 (p) cc_final: 0.8139 (t)
  outliers start: 24
  outliers final: 21
  residues processed: 222
  average time/residue: 0.1500
  time to fit residues: 45.5620
Evaluate side-chains
  223 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 202
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue   94 CYS
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  159 GLU
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  211 GLU
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  240 LYS
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue  138 HIS
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  350 LEU
Chi-restraints excluded: chain B residue  358 GLU
Chi-restraints excluded: chain B residue  392 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 26 optimal weight:    4.9990
   chunk 74 optimal weight:    0.6980
   chunk 73 optimal weight:    0.0870
   chunk 10 optimal weight:    0.9980
   chunk 27 optimal weight:    0.5980
   chunk 0 optimal weight:    6.9990
   chunk 57 optimal weight:    0.5980
   chunk 77 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 71 optimal weight:    0.7980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
B 138 HIS
B 324 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.156321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.135442 restraints weight = 10059.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.139008 restraints weight = 5981.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.141439 restraints weight = 4094.872|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.2383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   6390  Z= 0.136
  Angle     :  0.740  14.887   8736  Z= 0.329
  Chirality :  0.041   0.217   1072
  Planarity :  0.005   0.052   1086
  Dihedral  :  6.577  59.033   1018
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 22.66 %
    Favored  : 73.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.26 (0.30), residues: 790
  helix:  2.78 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.51 (0.54), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B 258 
 HIS   0.016   0.001   HIS B 138 
 PHE   0.016   0.001   PHE B 208 
 TYR   0.018   0.001   TYR A 299 
 ARG   0.006   0.000   ARG B 382 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00501 (    6)
  link_NAG-ASN         : angle       1.24024 (   18)
  link_BETA1-4         : bond        0.01937 (    2)
  link_BETA1-4         : angle       4.28789 (    6)
  hydrogen bonds       : bond        0.03703 (  552)
  hydrogen bonds       : angle       3.92615 ( 1656)
  SS BOND              : bond        0.00233 (    4)
  SS BOND              : angle       1.45638 (    8)
  covalent geometry    : bond        0.00297 ( 6378)
  covalent geometry    : angle       0.72878 ( 8704)

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

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 202
  time to evaluate  : 0.655 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 TYR cc_start: 0.8084 (t80) cc_final: 0.7848 (t80)
REVERT: A  273 ASP cc_start: 0.7663 (t70) cc_final: 0.7137 (t70)
REVERT: A  330 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8610 (mt)
REVERT: A  381 LEU cc_start: 0.8574 (mt) cc_final: 0.8014 (mt)
REVERT: A  402 SER cc_start: 0.8618 (p) cc_final: 0.8130 (t)
REVERT: B  134 SER cc_start: 0.9012 (m) cc_final: 0.7943 (t)
REVERT: B  240 LYS cc_start: 0.7477 (mttp) cc_final: 0.7191 (mttp)
REVERT: B  304 ASN cc_start: 0.8204 (m-40) cc_final: 0.7883 (t0)
REVERT: B  381 LEU cc_start: 0.8700 (mt) cc_final: 0.8031 (mt)
REVERT: B  402 SER cc_start: 0.8655 (p) cc_final: 0.8107 (t)
  outliers start: 26
  outliers final: 20
  residues processed: 213
  average time/residue: 0.1880
  time to fit residues: 56.2535
Evaluate side-chains
  216 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 195
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue   94 CYS
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  159 GLU
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  211 GLU
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  240 LYS
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue  138 HIS
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  350 LEU
Chi-restraints excluded: chain B residue  392 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 21 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9990
   chunk 49 optimal weight:    4.9990
   chunk 37 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 75 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9980
   chunk 67 optimal weight:    0.0040
   chunk 77 optimal weight:    5.9990
   overall best weight:    0.6794

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

Flipped N/Q/H residues before XYZ refinement:
A  17 HIS
** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 324 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.156041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.135134 restraints weight = 10018.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.138641 restraints weight = 5972.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.141049 restraints weight = 4092.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.2455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   6390  Z= 0.144
  Angle     :  0.763  15.589   8736  Z= 0.342
  Chirality :  0.042   0.318   1072
  Planarity :  0.005   0.053   1086
  Dihedral  :  6.459  57.966   1018
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 24.62 %
    Favored  : 71.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.22 (0.30), residues: 790
  helix:  2.74 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.47 (0.53), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP B 258 
 HIS   0.011   0.001   HIS B 138 
 PHE   0.017   0.001   PHE B 208 
 TYR   0.021   0.002   TYR A 299 
 ARG   0.005   0.000   ARG B 382 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00462 (    6)
  link_NAG-ASN         : angle       1.50710 (   18)
  link_BETA1-4         : bond        0.02008 (    2)
  link_BETA1-4         : angle       4.36351 (    6)
  hydrogen bonds       : bond        0.03718 (  552)
  hydrogen bonds       : angle       3.97116 ( 1656)
  SS BOND              : bond        0.00224 (    4)
  SS BOND              : angle       1.52013 (    8)
  covalent geometry    : bond        0.00320 ( 6378)
  covalent geometry    : angle       0.75133 ( 8704)

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

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 202
  time to evaluate  : 0.798 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 TYR cc_start: 0.8110 (t80) cc_final: 0.7853 (t80)
REVERT: A  139 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8914 (tt)
REVERT: A  273 ASP cc_start: 0.7680 (t70) cc_final: 0.7192 (t70)
REVERT: A  330 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8567 (mt)
REVERT: A  381 LEU cc_start: 0.8605 (mt) cc_final: 0.8009 (mt)
REVERT: A  402 SER cc_start: 0.8621 (p) cc_final: 0.8075 (t)
REVERT: B  134 SER cc_start: 0.8982 (m) cc_final: 0.7899 (t)
REVERT: B  240 LYS cc_start: 0.7501 (mttp) cc_final: 0.7213 (mttp)
REVERT: B  246 MET cc_start: 0.7262 (ppp) cc_final: 0.5860 (ppp)
REVERT: B  304 ASN cc_start: 0.8179 (m-40) cc_final: 0.7888 (t0)
REVERT: B  381 LEU cc_start: 0.8710 (mt) cc_final: 0.8007 (mt)
REVERT: B  402 SER cc_start: 0.8666 (p) cc_final: 0.8102 (t)
  outliers start: 23
  outliers final: 20
  residues processed: 214
  average time/residue: 0.1597
  time to fit residues: 47.6539
Evaluate side-chains
  219 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 197
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue   94 CYS
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  159 GLU
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  211 GLU
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  240 LYS
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  350 LEU
Chi-restraints excluded: chain B residue  392 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 32 optimal weight:    0.5980
   chunk 68 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9980
   chunk 29 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 324 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.155214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.135560 restraints weight = 9985.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.138659 restraints weight = 6247.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.140608 restraints weight = 4422.803|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.2565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071   6390  Z= 0.147
  Angle     :  0.768  15.378   8736  Z= 0.344
  Chirality :  0.043   0.311   1072
  Planarity :  0.005   0.052   1086
  Dihedral  :  6.357  56.959   1018
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 25.23 %
    Favored  : 71.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.26 (0.30), residues: 790
  helix:  2.74 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.29 (0.54), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B 258 
 HIS   0.005   0.001   HIS B 326 
 PHE   0.017   0.001   PHE B 208 
 TYR   0.023   0.002   TYR A 299 
 ARG   0.006   0.000   ARG B 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00561 (    6)
  link_NAG-ASN         : angle       1.49338 (   18)
  link_BETA1-4         : bond        0.01840 (    2)
  link_BETA1-4         : angle       4.35299 (    6)
  hydrogen bonds       : bond        0.03727 (  552)
  hydrogen bonds       : angle       3.97957 ( 1656)
  SS BOND              : bond        0.00249 (    4)
  SS BOND              : angle       1.57846 (    8)
  covalent geometry    : bond        0.00328 ( 6378)
  covalent geometry    : angle       0.75680 ( 8704)

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

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 201
  time to evaluate  : 0.979 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 TYR cc_start: 0.8177 (t80) cc_final: 0.7894 (t80)
REVERT: A   61 PHE cc_start: 0.7131 (m-80) cc_final: 0.6873 (m-80)
REVERT: A  273 ASP cc_start: 0.7732 (t70) cc_final: 0.7200 (t70)
REVERT: A  287 GLN cc_start: 0.7800 (tp-100) cc_final: 0.7586 (tp-100)
REVERT: A  330 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8513 (mt)
REVERT: A  381 LEU cc_start: 0.8569 (mt) cc_final: 0.7960 (mt)
REVERT: A  402 SER cc_start: 0.8636 (p) cc_final: 0.8116 (t)
REVERT: B  134 SER cc_start: 0.9060 (m) cc_final: 0.8190 (t)
REVERT: B  240 LYS cc_start: 0.7471 (mttp) cc_final: 0.7200 (mttp)
REVERT: B  246 MET cc_start: 0.7313 (ppp) cc_final: 0.5914 (ppp)
REVERT: B  304 ASN cc_start: 0.8144 (m-40) cc_final: 0.7906 (t0)
REVERT: B  381 LEU cc_start: 0.8676 (mt) cc_final: 0.7992 (mt)
REVERT: B  402 SER cc_start: 0.8712 (p) cc_final: 0.8155 (t)
  outliers start: 24
  outliers final: 21
  residues processed: 215
  average time/residue: 0.1702
  time to fit residues: 51.2917
Evaluate side-chains
  214 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 192
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue   94 CYS
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  159 GLU
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  211 GLU
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  240 LYS
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  350 LEU
Chi-restraints excluded: chain B residue  392 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 59 optimal weight:    0.9980
   chunk 75 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   chunk 1 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   chunk 27 optimal weight:    0.5980
   chunk 15 optimal weight:    3.9990
   chunk 16 optimal weight:    0.3980
   chunk 41 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 324 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.155357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.136977 restraints weight = 10024.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.138178 restraints weight = 6730.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.139621 restraints weight = 5487.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.2642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.080   6390  Z= 0.152
  Angle     :  0.797  15.296   8736  Z= 0.358
  Chirality :  0.043   0.270   1072
  Planarity :  0.005   0.051   1086
  Dihedral  :  6.362  56.701   1018
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 25.53 %
    Favored  : 70.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.24 (0.30), residues: 790
  helix:  2.70 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.10 (0.56), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP B 258 
 HIS   0.005   0.001   HIS B 326 
 PHE   0.016   0.001   PHE B 208 
 TYR   0.024   0.002   TYR A 299 
 ARG   0.005   0.000   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00732 (    6)
  link_NAG-ASN         : angle       2.14029 (   18)
  link_BETA1-4         : bond        0.01917 (    2)
  link_BETA1-4         : angle       4.45929 (    6)
  hydrogen bonds       : bond        0.03801 (  552)
  hydrogen bonds       : angle       4.02694 ( 1656)
  SS BOND              : bond        0.00216 (    4)
  SS BOND              : angle       1.62711 (    8)
  covalent geometry    : bond        0.00343 ( 6378)
  covalent geometry    : angle       0.78187 ( 8704)

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

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 197
  time to evaluate  : 0.670 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 TYR cc_start: 0.8219 (t80) cc_final: 0.7941 (t80)
REVERT: A   61 PHE cc_start: 0.7096 (m-80) cc_final: 0.6852 (m-80)
REVERT: A   95 ILE cc_start: 0.8209 (mp) cc_final: 0.7933 (mm)
REVERT: A  189 LEU cc_start: 0.8478 (mm) cc_final: 0.8275 (mm)
REVERT: A  200 LEU cc_start: 0.8466 (mt) cc_final: 0.8015 (mt)
REVERT: A  204 GLU cc_start: 0.5965 (tt0) cc_final: 0.5556 (pt0)
REVERT: A  273 ASP cc_start: 0.7727 (t70) cc_final: 0.7219 (t70)
REVERT: A  330 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8551 (mt)
REVERT: A  381 LEU cc_start: 0.8585 (mt) cc_final: 0.7962 (mt)
REVERT: A  402 SER cc_start: 0.8603 (p) cc_final: 0.7995 (t)
REVERT: B  134 SER cc_start: 0.9077 (m) cc_final: 0.8052 (t)
REVERT: B  240 LYS cc_start: 0.7475 (mttp) cc_final: 0.7173 (mttp)
REVERT: B  246 MET cc_start: 0.7370 (ppp) cc_final: 0.6044 (ppp)
REVERT: B  304 ASN cc_start: 0.8170 (m-40) cc_final: 0.7884 (t0)
REVERT: B  381 LEU cc_start: 0.8710 (mt) cc_final: 0.8023 (mt)
REVERT: B  402 SER cc_start: 0.8678 (p) cc_final: 0.8066 (t)
  outliers start: 25
  outliers final: 21
  residues processed: 210
  average time/residue: 0.1602
  time to fit residues: 47.8552
Evaluate side-chains
  217 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 195
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue   94 CYS
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  159 GLU
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  211 GLU
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  240 LYS
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  350 LEU
Chi-restraints excluded: chain B residue  358 GLU
Chi-restraints excluded: chain B residue  392 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 36 optimal weight:    0.7980
   chunk 38 optimal weight:    5.9990
   chunk 17 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0870
   chunk 11 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.7358

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 360 ASN
B 324 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.156347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.138001 restraints weight = 9998.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.142499 restraints weight = 5883.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.143303 restraints weight = 3557.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.2705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083   6390  Z= 0.151
  Angle     :  0.800  15.776   8736  Z= 0.360
  Chirality :  0.043   0.287   1072
  Planarity :  0.005   0.050   1086
  Dihedral  :  6.348  54.605   1018
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 25.83 %
    Favored  : 70.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.22 (0.30), residues: 790
  helix:  2.67 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.05 (0.57), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP B 258 
 HIS   0.005   0.001   HIS B 326 
 PHE   0.016   0.001   PHE B 208 
 TYR   0.024   0.002   TYR A 299 
 ARG   0.004   0.000   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00772 (    6)
  link_NAG-ASN         : angle       2.06665 (   18)
  link_BETA1-4         : bond        0.01839 (    2)
  link_BETA1-4         : angle       4.49112 (    6)
  hydrogen bonds       : bond        0.03767 (  552)
  hydrogen bonds       : angle       4.02778 ( 1656)
  SS BOND              : bond        0.00247 (    4)
  SS BOND              : angle       1.69889 (    8)
  covalent geometry    : bond        0.00342 ( 6378)
  covalent geometry    : angle       0.78596 ( 8704)

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

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 203
  time to evaluate  : 0.668 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 TYR cc_start: 0.8109 (t80) cc_final: 0.7869 (t80)
REVERT: A   61 PHE cc_start: 0.7031 (m-80) cc_final: 0.6789 (m-80)
REVERT: A  204 GLU cc_start: 0.5858 (tt0) cc_final: 0.5492 (pt0)
REVERT: A  273 ASP cc_start: 0.7721 (t70) cc_final: 0.7207 (t70)
REVERT: A  330 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8604 (mt)
REVERT: A  381 LEU cc_start: 0.8602 (mt) cc_final: 0.7976 (mt)
REVERT: A  402 SER cc_start: 0.8607 (p) cc_final: 0.7968 (t)
REVERT: B  134 SER cc_start: 0.9034 (m) cc_final: 0.8115 (t)
REVERT: B  240 LYS cc_start: 0.7439 (mttp) cc_final: 0.7159 (mttp)
REVERT: B  246 MET cc_start: 0.7188 (ppp) cc_final: 0.6083 (ppp)
REVERT: B  381 LEU cc_start: 0.8716 (mt) cc_final: 0.8034 (mt)
REVERT: B  402 SER cc_start: 0.8663 (p) cc_final: 0.8032 (t)
  outliers start: 23
  outliers final: 22
  residues processed: 214
  average time/residue: 0.1925
  time to fit residues: 59.0338
Evaluate side-chains
  222 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 199
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue   94 CYS
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  159 GLU
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  211 GLU
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  240 LYS
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  350 LEU
Chi-restraints excluded: chain B residue  358 GLU
Chi-restraints excluded: chain B residue  392 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 48 optimal weight:    0.3980
   chunk 39 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 34 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 11 optimal weight:    0.5980
   chunk 58 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   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 287 GLN
** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 324 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.156333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.135320 restraints weight = 10081.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.138851 restraints weight = 6018.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.141144 restraints weight = 4112.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.2753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6390  Z= 0.146
  Angle     :  0.793  16.098   8736  Z= 0.355
  Chirality :  0.043   0.259   1072
  Planarity :  0.005   0.049   1086
  Dihedral  :  6.300  53.851   1018
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 25.83 %
    Favored  : 70.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.19 (0.30), residues: 790
  helix:  2.69 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.33 (0.54), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP B 258 
 HIS   0.005   0.001   HIS B 326 
 PHE   0.015   0.001   PHE B 208 
 TYR   0.023   0.002   TYR A 299 
 ARG   0.004   0.000   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00724 (    6)
  link_NAG-ASN         : angle       1.93763 (   18)
  link_BETA1-4         : bond        0.01851 (    2)
  link_BETA1-4         : angle       4.58372 (    6)
  hydrogen bonds       : bond        0.03738 (  552)
  hydrogen bonds       : angle       3.96595 ( 1656)
  SS BOND              : bond        0.00302 (    4)
  SS BOND              : angle       1.67137 (    8)
  covalent geometry    : bond        0.00318 ( 6378)
  covalent geometry    : angle       0.77890 ( 8704)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2317.14 seconds
wall clock time: 42 minutes 19.03 seconds (2539.03 seconds total)