Starting phenix.real_space_refine
on Tue Mar  3 14:44:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p5j_13200/03_2026/7p5j_13200.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p5j_13200/03_2026/7p5j_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_13200/03_2026/7p5j_13200.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p5j_13200/03_2026/7p5j_13200.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p5j_13200/03_2026/7p5j_13200.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p5j_13200/03_2026/7p5j_13200.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.58, per 1000 atoms: 0.25
  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: 0.57
  Conformation dependent library (CDL) restraints added in 214.1 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: 0.09
  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: 0.84

  Time building geometry restraints manager: 0.73 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.810
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.790
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.65 (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
 ARG   0.004   0.000   ARG A 314 
 TYR   0.026   0.002   TYR A 299 
 PHE   0.029   0.002   PHE B 208 
 TRP   0.016   0.001   TRP A 258 
 HIS   0.004   0.001   HIS B 128 

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

*********************** 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  : 0.210 
Fit side-chains
   revert: symmetry clash
REVERT: A  273 ASP cc_start: 0.7621 (t70) cc_final: 0.6956 (t70)
REVERT: A  350 LEU cc_start: 0.8933 (mt) cc_final: 0.8660 (mt)
REVERT: B   24 PHE cc_start: 0.7468 (p90) cc_final: 0.7260 (p90)
REVERT: B   40 TYR cc_start: 0.7595 (t80) cc_final: 0.7383 (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: 0.8682 (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: 0.7624 (m-40)
  outliers start: 4
  outliers final: 2
  residues processed: 241
  average time/residue: 0.0569
  time to fit residues: 19.3550
Evaluate side-chains
  203 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 201
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.5980
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3818 r_free = 0.3818 target = 0.155690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.134622 restraints weight = 10104.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.137940 restraints weight = 5976.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.140411 restraints weight = 4134.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.141916 restraints weight = 3131.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.143091 restraints weight = 2584.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.1362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6390  Z= 0.158
  Angle     :  0.701   9.735   8736  Z= 0.326
  Chirality :  0.044   0.252   1072
  Planarity :  0.005   0.076   1086
  Dihedral  : 10.895  77.560   1024
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 14.65 %
    Favored  : 83.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.12 (0.30), residues: 790
  helix:  2.66 (0.20), residues: 662
  sheet:  None (None), residues: 0
  loop : -1.40 (0.56), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 371 
 TYR   0.018   0.002   TYR A 377 
 PHE   0.034   0.002   PHE A 208 
 TRP   0.018   0.001   TRP B 258 
 HIS   0.005   0.001   HIS B 128 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 6378)
  covalent geometry    : angle       0.69253 ( 8704)
  SS BOND              : bond        0.00306 (    4)
  SS BOND              : angle       1.07764 (    8)
  hydrogen bonds       : bond        0.04466 (  552)
  hydrogen bonds       : angle       4.22946 ( 1656)
  link_BETA1-4         : bond        0.01753 (    2)
  link_BETA1-4         : angle       3.65723 (    6)
  link_NAG-ASN         : bond        0.00494 (    6)
  link_NAG-ASN         : angle       1.38965 (   18)

*********************** 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
  229 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 215
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8329 (mp)
REVERT: A  131 HIS cc_start: 0.8190 (t70) cc_final: 0.7946 (t70)
REVERT: A  273 ASP cc_start: 0.7582 (t70) cc_final: 0.7299 (t70)
REVERT: B  134 SER cc_start: 0.8964 (m) cc_final: 0.8268 (t)
REVERT: B  304 ASN cc_start: 0.8169 (m-40) cc_final: 0.7686 (m-40)
REVERT: B  381 LEU cc_start: 0.8374 (mt) cc_final: 0.8172 (mp)
  outliers start: 14
  outliers final: 10
  residues processed: 219
  average time/residue: 0.0568
  time to fit residues: 17.5552
Evaluate side-chains
  215 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 204
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   94 CYS
Chi-restraints excluded: chain A residue   95 ILE
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  279 ASP
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 72 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 57 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 40 optimal weight:   20.0000
   overall best weight:    1.3386

-------------------------------------------------------------------------------
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 = 0.3787 r_free = 0.3787 target = 0.152957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.131854 restraints weight = 10166.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.135121 restraints weight = 6147.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.137372 restraints weight = 4290.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.138913 restraints weight = 3295.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.140021 restraints weight = 2730.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.1775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6390  Z= 0.180
  Angle     :  0.732  10.324   8736  Z= 0.339
  Chirality :  0.042   0.192   1072
  Planarity :  0.005   0.064   1086
  Dihedral  :  8.471  56.849   1018
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 18.58 %
    Favored  : 78.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.10 (0.30), residues: 790
  helix:  2.61 (0.20), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.21 (0.59), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 320 
 TYR   0.024   0.002   TYR A 299 
 PHE   0.034   0.002   PHE B 208 
 TRP   0.019   0.002   TRP B 258 
 HIS   0.006   0.001   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 6378)
  covalent geometry    : angle       0.72302 ( 8704)
  SS BOND              : bond        0.00351 (    4)
  SS BOND              : angle       1.09729 (    8)
  hydrogen bonds       : bond        0.04217 (  552)
  hydrogen bonds       : angle       4.23992 ( 1656)
  link_BETA1-4         : bond        0.02070 (    2)
  link_BETA1-4         : angle       3.92666 (    6)
  link_NAG-ASN         : bond        0.00375 (    6)
  link_NAG-ASN         : angle       1.16812 (   18)

*********************** 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
  235 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 218
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 TYR cc_start: 0.7827 (t80) cc_final: 0.7572 (t80)
REVERT: A   95 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8270 (mm)
REVERT: A  114 GLU cc_start: 0.8725 (tp30) cc_final: 0.8457 (tp30)
REVERT: A  273 ASP cc_start: 0.7689 (t70) cc_final: 0.7293 (t70)
REVERT: A  328 GLN cc_start: 0.8370 (pm20) cc_final: 0.8153 (pm20)
REVERT: A  402 SER cc_start: 0.8802 (p) cc_final: 0.8257 (t)
REVERT: B  134 SER cc_start: 0.9055 (m) cc_final: 0.8176 (t)
REVERT: B  240 LYS cc_start: 0.7596 (mttp) cc_final: 0.7283 (mttp)
REVERT: B  304 ASN cc_start: 0.8200 (m-40) cc_final: 0.7757 (m-40)
REVERT: B  381 LEU cc_start: 0.8591 (mt) cc_final: 0.8293 (mt)
REVERT: B  402 SER cc_start: 0.8711 (p) cc_final: 0.8188 (t)
  outliers start: 17
  outliers final: 14
  residues processed: 224
  average time/residue: 0.0580
  time to fit residues: 18.1600
Evaluate side-chains
  221 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 206
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
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   95 ILE
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  159 GLU
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  211 GLU
Chi-restraints excluded: chain A residue  225 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
Chi-restraints excluded: chain B residue  358 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 72 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 49 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   chunk 52 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 69 optimal weight:    0.8980
   overall best weight:    0.9786

-------------------------------------------------------------------------------
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 = 0.3812 r_free = 0.3812 target = 0.154272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.134178 restraints weight = 10090.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.137306 restraints weight = 6321.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.139400 restraints weight = 4486.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.140848 restraints weight = 3496.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.141740 restraints weight = 2918.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.1988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   6390  Z= 0.157
  Angle     :  0.722  10.641   8736  Z= 0.330
  Chirality :  0.042   0.241   1072
  Planarity :  0.005   0.062   1086
  Dihedral  :  7.356  55.972   1018
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 19.79 %
    Favored  : 77.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.12 (0.30), residues: 790
  helix:  2.64 (0.20), residues: 666
  sheet:  None (None), residues: 0
  loop : -1.38 (0.57), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 177 
 TYR   0.026   0.002   TYR A 299 
 PHE   0.033   0.002   PHE B 208 
 TRP   0.020   0.001   TRP B 258 
 HIS   0.005   0.001   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 6378)
  covalent geometry    : angle       0.71181 ( 8704)
  SS BOND              : bond        0.00419 (    4)
  SS BOND              : angle       1.16668 (    8)
  hydrogen bonds       : bond        0.03995 (  552)
  hydrogen bonds       : angle       4.14243 ( 1656)
  link_BETA1-4         : bond        0.02071 (    2)
  link_BETA1-4         : angle       4.17186 (    6)
  link_NAG-ASN         : bond        0.00451 (    6)
  link_NAG-ASN         : angle       1.19208 (   18)

*********************** 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
  226 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 206
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
REVERT: A  114 GLU cc_start: 0.8734 (tp30) cc_final: 0.8425 (tp30)
REVERT: A  273 ASP cc_start: 0.7727 (t70) cc_final: 0.7161 (t70)
REVERT: A  402 SER cc_start: 0.8736 (p) cc_final: 0.8255 (t)
REVERT: B  134 SER cc_start: 0.9064 (m) cc_final: 0.8267 (t)
REVERT: B  240 LYS cc_start: 0.7494 (mttp) cc_final: 0.7193 (mttp)
REVERT: B  304 ASN cc_start: 0.8353 (m-40) cc_final: 0.7852 (t0)
REVERT: B  309 ASN cc_start: 0.8779 (t0) cc_final: 0.8518 (t0)
REVERT: B  381 LEU cc_start: 0.8445 (mt) cc_final: 0.7971 (mt)
REVERT: B  402 SER cc_start: 0.8666 (p) cc_final: 0.8214 (t)
  outliers start: 20
  outliers final: 17
  residues processed: 215
  average time/residue: 0.0575
  time to fit residues: 17.4626
Evaluate side-chains
  220 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 203
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  200 LEU
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  396 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
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 21 optimal weight:    4.9990
   chunk 68 optimal weight:    4.9990
   chunk 69 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   chunk 60 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 75 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   overall best weight:    1.9588

-------------------------------------------------------------------------------
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 128 HIS
B 138 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.148685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.128675 restraints weight = 10374.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.131601 restraints weight = 6532.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.133738 restraints weight = 4673.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.134969 restraints weight = 3649.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.135985 restraints weight = 3082.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.2382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069   6390  Z= 0.231
  Angle     :  0.829  13.171   8736  Z= 0.376
  Chirality :  0.045   0.202   1072
  Planarity :  0.006   0.063   1086
  Dihedral  :  7.393  59.893   1018
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 19.64 %
    Favored  : 75.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.81 (0.30), residues: 790
  helix:  2.45 (0.20), residues: 662
  sheet:  None (None), residues: 0
  loop : -1.46 (0.55), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 213 
 TYR   0.038   0.003   TYR A 299 
 PHE   0.028   0.002   PHE B 208 
 TRP   0.022   0.002   TRP B 258 
 HIS   0.010   0.002   HIS B 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00516 ( 6378)
  covalent geometry    : angle       0.81916 ( 8704)
  SS BOND              : bond        0.00460 (    4)
  SS BOND              : angle       1.36943 (    8)
  hydrogen bonds       : bond        0.04289 (  552)
  hydrogen bonds       : angle       4.38070 ( 1656)
  link_BETA1-4         : bond        0.02127 (    2)
  link_BETA1-4         : angle       4.42277 (    6)
  link_NAG-ASN         : bond        0.00327 (    6)
  link_NAG-ASN         : angle       1.30379 (   18)

*********************** 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
  239 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 207
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 TYR cc_start: 0.7953 (t80) cc_final: 0.7259 (t80)
REVERT: A   61 PHE cc_start: 0.7055 (m-80) cc_final: 0.6834 (m-80)
REVERT: A  273 ASP cc_start: 0.7734 (t70) cc_final: 0.6910 (t70)
REVERT: A  330 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8614 (mt)
REVERT: A  402 SER cc_start: 0.8615 (p) cc_final: 0.8136 (t)
REVERT: B  134 SER cc_start: 0.9240 (m) cc_final: 0.8225 (t)
REVERT: B  138 HIS cc_start: 0.7562 (OUTLIER) cc_final: 0.7126 (t70)
REVERT: B  139 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.9018 (mt)
REVERT: B  304 ASN cc_start: 0.8325 (m-40) cc_final: 0.7926 (m-40)
REVERT: B  381 LEU cc_start: 0.8618 (mt) cc_final: 0.8118 (mt)
REVERT: B  402 SER cc_start: 0.8617 (p) cc_final: 0.8075 (t)
  outliers start: 32
  outliers final: 23
  residues processed: 220
  average time/residue: 0.0529
  time to fit residues: 16.4356
Evaluate side-chains
  225 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 199
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
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  113 SER
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  159 GLU
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  200 LEU
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 A residue  240 LYS
Chi-restraints excluded: chain A residue  279 ASP
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  396 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  142 GLU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  267 THR
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  350 LEU
Chi-restraints excluded: chain B residue  358 GLU
Chi-restraints excluded: chain B residue  386 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 29 optimal weight:    0.7980
   chunk 63 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   chunk 49 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 71 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   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 326 HIS
** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 128 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.153273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.132217 restraints weight = 10105.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.135667 restraints weight = 6049.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.137944 restraints weight = 4182.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.139657 restraints weight = 3212.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.140723 restraints weight = 2629.280|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.2427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   6390  Z= 0.152
  Angle     :  0.762  14.181   8736  Z= 0.342
  Chirality :  0.041   0.197   1072
  Planarity :  0.005   0.055   1086
  Dihedral  :  7.046  59.391   1018
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 21.15 %
    Favored  : 74.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.03 (0.30), residues: 790
  helix:  2.59 (0.20), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.44 (0.56), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 334 
 TYR   0.026   0.002   TYR A 299 
 PHE   0.034   0.002   PHE B 208 
 TRP   0.024   0.001   TRP B 258 
 HIS   0.013   0.001   HIS B 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 6378)
  covalent geometry    : angle       0.75017 ( 8704)
  SS BOND              : bond        0.00497 (    4)
  SS BOND              : angle       1.47979 (    8)
  hydrogen bonds       : bond        0.03976 (  552)
  hydrogen bonds       : angle       4.14849 ( 1656)
  link_BETA1-4         : bond        0.01972 (    2)
  link_BETA1-4         : angle       4.50613 (    6)
  link_NAG-ASN         : bond        0.00466 (    6)
  link_NAG-ASN         : angle       1.26701 (   18)

*********************** 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
  244 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 215
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 TYR cc_start: 0.7751 (t80) cc_final: 0.7299 (t80)
REVERT: A   61 PHE cc_start: 0.6885 (m-80) cc_final: 0.6684 (m-80)
REVERT: A  114 GLU cc_start: 0.8640 (tp30) cc_final: 0.8420 (tp30)
REVERT: A  273 ASP cc_start: 0.7632 (t70) cc_final: 0.7008 (t70)
REVERT: A  330 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8691 (mt)
REVERT: A  381 LEU cc_start: 0.8621 (mt) cc_final: 0.8308 (mp)
REVERT: A  402 SER cc_start: 0.8598 (p) cc_final: 0.8073 (t)
REVERT: B  134 SER cc_start: 0.8968 (m) cc_final: 0.7919 (t)
REVERT: B  304 ASN cc_start: 0.8240 (m-40) cc_final: 0.7816 (m-40)
REVERT: B  353 THR cc_start: 0.8418 (t) cc_final: 0.8023 (t)
REVERT: B  381 LEU cc_start: 0.8566 (mt) cc_final: 0.8056 (mt)
REVERT: B  402 SER cc_start: 0.8600 (p) cc_final: 0.8003 (t)
  outliers start: 29
  outliers final: 21
  residues processed: 229
  average time/residue: 0.0581
  time to fit residues: 18.5919
Evaluate side-chains
  228 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 206
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
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  200 LEU
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  142 GLU
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  350 LEU
Chi-restraints excluded: chain B residue  358 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 21 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 23 optimal weight:    8.9990
   chunk 4 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 6 optimal weight:    5.9990
   chunk 72 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 54 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    1.7586

-------------------------------------------------------------------------------
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 128 HIS
B 138 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.150202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.131624 restraints weight = 10202.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.133100 restraints weight = 7036.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.134426 restraints weight = 5544.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.136330 restraints weight = 4211.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.136553 restraints weight = 3492.638|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.2666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.082   6390  Z= 0.216
  Angle     :  0.834  15.408   8736  Z= 0.378
  Chirality :  0.044   0.218   1072
  Planarity :  0.005   0.049   1086
  Dihedral  :  7.264  58.111   1018
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 22.96 %
    Favored  : 72.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.86 (0.30), residues: 790
  helix:  2.47 (0.20), residues: 660
  sheet:  None (None), residues: 0
  loop : -1.32 (0.58), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 177 
 TYR   0.034   0.002   TYR A 299 
 PHE   0.028   0.002   PHE B 208 
 TRP   0.024   0.002   TRP B 258 
 HIS   0.007   0.001   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00490 ( 6378)
  covalent geometry    : angle       0.82366 ( 8704)
  SS BOND              : bond        0.00468 (    4)
  SS BOND              : angle       1.51729 (    8)
  hydrogen bonds       : bond        0.04201 (  552)
  hydrogen bonds       : angle       4.30577 ( 1656)
  link_BETA1-4         : bond        0.01908 (    2)
  link_BETA1-4         : angle       4.57258 (    6)
  link_NAG-ASN         : bond        0.00418 (    6)
  link_NAG-ASN         : angle       1.35735 (   18)

*********************** 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
  237 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 207
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 TYR cc_start: 0.8022 (t80) cc_final: 0.7389 (t80)
REVERT: A  273 ASP cc_start: 0.7752 (t70) cc_final: 0.6916 (t70)
REVERT: A  402 SER cc_start: 0.8598 (p) cc_final: 0.8125 (t)
REVERT: B  134 SER cc_start: 0.9071 (m) cc_final: 0.8258 (t)
REVERT: B  139 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8866 (mt)
REVERT: B  304 ASN cc_start: 0.8370 (m-40) cc_final: 0.7938 (m-40)
REVERT: B  353 THR cc_start: 0.8585 (t) cc_final: 0.8241 (t)
REVERT: B  402 SER cc_start: 0.8620 (p) cc_final: 0.8031 (t)
  outliers start: 30
  outliers final: 24
  residues processed: 219
  average time/residue: 0.0586
  time to fit residues: 18.2509
Evaluate side-chains
  229 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 204
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
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  126 LEU
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  200 LEU
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 A residue  240 LYS
Chi-restraints excluded: chain A residue  279 ASP
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  126 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  142 GLU
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  350 LEU
Chi-restraints excluded: chain B residue  358 GLU
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 24 optimal weight:    0.5980
   chunk 73 optimal weight:    0.9990
   chunk 68 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9980
   chunk 38 optimal weight:    4.9990
   chunk 4 optimal weight:    5.9990
   chunk 33 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 77 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 128 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.153657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.132777 restraints weight = 10159.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.136253 restraints weight = 6145.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.138610 restraints weight = 4227.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.140273 restraints weight = 3214.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.141308 restraints weight = 2619.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.2675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   6390  Z= 0.153
  Angle     :  0.803  15.439   8736  Z= 0.357
  Chirality :  0.043   0.250   1072
  Planarity :  0.005   0.048   1086
  Dihedral  :  6.838  55.230   1018
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 24.17 %
    Favored  : 71.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.01 (0.30), residues: 790
  helix:  2.61 (0.20), residues: 660
  sheet:  None (None), residues: 0
  loop : -1.45 (0.57), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 177 
 TYR   0.023   0.002   TYR A 299 
 PHE   0.034   0.002   PHE B 208 
 TRP   0.025   0.001   TRP B 258 
 HIS   0.006   0.001   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 6378)
  covalent geometry    : angle       0.79119 ( 8704)
  SS BOND              : bond        0.00310 (    4)
  SS BOND              : angle       1.44818 (    8)
  hydrogen bonds       : bond        0.03964 (  552)
  hydrogen bonds       : angle       4.15993 ( 1656)
  link_BETA1-4         : bond        0.01844 (    2)
  link_BETA1-4         : angle       4.76064 (    6)
  link_NAG-ASN         : bond        0.00494 (    6)
  link_NAG-ASN         : angle       1.26984 (   18)

*********************** 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
  238 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 209
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 TYR cc_start: 0.7896 (t80) cc_final: 0.7494 (t80)
REVERT: A  114 GLU cc_start: 0.8653 (tp30) cc_final: 0.8410 (tp30)
REVERT: A  273 ASP cc_start: 0.7728 (t70) cc_final: 0.7239 (t70)
REVERT: A  330 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8703 (mt)
REVERT: A  402 SER cc_start: 0.8577 (p) cc_final: 0.8017 (t)
REVERT: B  134 SER cc_start: 0.8953 (m) cc_final: 0.8119 (t)
REVERT: B  246 MET cc_start: 0.7144 (ppp) cc_final: 0.5730 (ppp)
REVERT: B  304 ASN cc_start: 0.8206 (m-40) cc_final: 0.7739 (m-40)
REVERT: B  330 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8670 (mt)
REVERT: B  353 THR cc_start: 0.8400 (t) cc_final: 0.8049 (t)
REVERT: B  381 LEU cc_start: 0.8783 (mt) cc_final: 0.8203 (mt)
REVERT: B  402 SER cc_start: 0.8630 (p) cc_final: 0.7987 (t)
  outliers start: 29
  outliers final: 20
  residues processed: 221
  average time/residue: 0.0582
  time to fit residues: 18.1319
Evaluate side-chains
  226 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 204
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
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  154 GLU
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  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 A residue  397 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  350 LEU
Chi-restraints excluded: chain B residue  358 GLU
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 72 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 54 optimal weight:    6.9990
   chunk 8 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 39 optimal weight:    0.4980
   chunk 5 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   overall best weight:    0.7984

-------------------------------------------------------------------------------
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 128 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.153549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.132881 restraints weight = 10067.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.136274 restraints weight = 6025.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.138650 restraints weight = 4151.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.140289 restraints weight = 3160.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.141339 restraints weight = 2578.498|
|-----------------------------------------------------------------------------|
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.2716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.086   6390  Z= 0.157
  Angle     :  0.806  15.539   8736  Z= 0.362
  Chirality :  0.043   0.250   1072
  Planarity :  0.004   0.046   1086
  Dihedral  :  6.649  55.236   1018
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 24.77 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.05 (0.30), residues: 790
  helix:  2.62 (0.19), residues: 658
  sheet:  None (None), residues: 0
  loop : -1.31 (0.57), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 177 
 TYR   0.016   0.002   TYR B  40 
 PHE   0.032   0.002   PHE B 208 
 TRP   0.015   0.001   TRP B 258 
 HIS   0.006   0.001   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 6378)
  covalent geometry    : angle       0.79382 ( 8704)
  SS BOND              : bond        0.00324 (    4)
  SS BOND              : angle       1.56685 (    8)
  hydrogen bonds       : bond        0.03954 (  552)
  hydrogen bonds       : angle       4.14868 ( 1656)
  link_BETA1-4         : bond        0.01869 (    2)
  link_BETA1-4         : angle       4.78005 (    6)
  link_NAG-ASN         : bond        0.00495 (    6)
  link_NAG-ASN         : angle       1.25173 (   18)

*********************** 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
  235 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 208
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 TYR cc_start: 0.7893 (t80) cc_final: 0.7471 (t80)
REVERT: A  114 GLU cc_start: 0.8660 (tp30) cc_final: 0.8413 (tp30)
REVERT: A  204 GLU cc_start: 0.5858 (tt0) cc_final: 0.5360 (pt0)
REVERT: A  273 ASP cc_start: 0.7709 (t70) cc_final: 0.7160 (t70)
REVERT: A  402 SER cc_start: 0.8591 (p) cc_final: 0.7985 (t)
REVERT: B  134 SER cc_start: 0.9030 (m) cc_final: 0.8150 (t)
REVERT: B  246 MET cc_start: 0.7156 (ppp) cc_final: 0.5799 (ppp)
REVERT: B  304 ASN cc_start: 0.7997 (m-40) cc_final: 0.7614 (m-40)
REVERT: B  330 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8692 (mt)
REVERT: B  353 THR cc_start: 0.8394 (t) cc_final: 0.8064 (t)
REVERT: B  381 LEU cc_start: 0.8720 (mt) cc_final: 0.8157 (mt)
REVERT: B  402 SER cc_start: 0.8648 (p) cc_final: 0.7992 (t)
  outliers start: 27
  outliers final: 24
  residues processed: 222
  average time/residue: 0.0569
  time to fit residues: 17.8357
Evaluate side-chains
  229 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 204
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   47 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  154 GLU
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  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 A residue  397 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  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 47 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9980
   chunk 41 optimal weight:    0.2980
   chunk 64 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 59 optimal weight:    5.9990
   chunk 21 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 53 optimal weight:    7.9990
   overall best weight:    1.2184

-------------------------------------------------------------------------------
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 128 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.152197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.131423 restraints weight = 10125.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.134834 restraints weight = 6059.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.137140 restraints weight = 4163.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.138730 restraints weight = 3190.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.139746 restraints weight = 2624.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.2790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.090   6390  Z= 0.178
  Angle     :  0.825  15.342   8736  Z= 0.373
  Chirality :  0.044   0.279   1072
  Planarity :  0.005   0.050   1086
  Dihedral  :  6.715  55.096   1018
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 25.23 %
    Favored  : 70.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.95 (0.30), residues: 790
  helix:  2.55 (0.19), residues: 660
  sheet:  None (None), residues: 0
  loop : -1.37 (0.57), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 177 
 TYR   0.018   0.002   TYR B  40 
 PHE   0.030   0.002   PHE B 208 
 TRP   0.015   0.001   TRP A 258 
 HIS   0.007   0.001   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 6378)
  covalent geometry    : angle       0.81257 ( 8704)
  SS BOND              : bond        0.00405 (    4)
  SS BOND              : angle       1.61894 (    8)
  hydrogen bonds       : bond        0.04046 (  552)
  hydrogen bonds       : angle       4.22675 ( 1656)
  link_BETA1-4         : bond        0.01783 (    2)
  link_BETA1-4         : angle       4.84688 (    6)
  link_NAG-ASN         : bond        0.00477 (    6)
  link_NAG-ASN         : angle       1.39572 (   18)

********************** 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
  233 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 207
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 TYR cc_start: 0.7943 (t80) cc_final: 0.7467 (t80)
REVERT: A  204 GLU cc_start: 0.5922 (tt0) cc_final: 0.5478 (pt0)
REVERT: A  273 ASP cc_start: 0.7743 (t70) cc_final: 0.7099 (t70)
REVERT: A  402 SER cc_start: 0.8616 (p) cc_final: 0.8008 (t)
REVERT: B  134 SER cc_start: 0.9124 (m) cc_final: 0.8266 (t)
REVERT: B  246 MET cc_start: 0.7210 (ppp) cc_final: 0.5861 (ppp)
REVERT: B  304 ASN cc_start: 0.8002 (m-40) cc_final: 0.7628 (m-40)
REVERT: B  330 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8669 (mt)
REVERT: B  353 THR cc_start: 0.8443 (t) cc_final: 0.8095 (t)
REVERT: B  402 SER cc_start: 0.8630 (p) cc_final: 0.8034 (t)
  outliers start: 26
  outliers final: 23
  residues processed: 219
  average time/residue: 0.0548
  time to fit residues: 17.0293
Evaluate side-chains
  228 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 204
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   47 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  154 GLU
Chi-restraints excluded: chain A residue  195 VAL
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 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 A residue  397 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  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 65 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 54 optimal weight:    6.9990
   chunk 48 optimal weight:    6.9990
   chunk 12 optimal weight:    0.8980
   chunk 62 optimal weight:    6.9990
   chunk 69 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   overall best weight:    1.1382

-------------------------------------------------------------------------------
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 128 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.152390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.131603 restraints weight = 10130.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.134998 restraints weight = 6077.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.137300 restraints weight = 4204.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.138795 restraints weight = 3225.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.139905 restraints weight = 2669.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.2823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.086   6390  Z= 0.175
  Angle     :  0.835  15.746   8736  Z= 0.378
  Chirality :  0.044   0.292   1072
  Planarity :  0.005   0.049   1086
  Dihedral  :  6.709  54.601   1018
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 25.38 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.88 (0.30), residues: 790
  helix:  2.52 (0.19), residues: 662
  sheet:  None (None), residues: 0
  loop : -1.59 (0.56), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 177 
 TYR   0.019   0.002   TYR A 299 
 PHE   0.030   0.002   PHE B 208 
 TRP   0.016   0.001   TRP A 258 
 HIS   0.007   0.001   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 6378)
  covalent geometry    : angle       0.82300 ( 8704)
  SS BOND              : bond        0.00346 (    4)
  SS BOND              : angle       1.60056 (    8)
  hydrogen bonds       : bond        0.04017 (  552)
  hydrogen bonds       : angle       4.23169 ( 1656)
  link_BETA1-4         : bond        0.01859 (    2)
  link_BETA1-4         : angle       4.83976 (    6)
  link_NAG-ASN         : bond        0.00462 (    6)
  link_NAG-ASN         : angle       1.39288 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 978.21 seconds
wall clock time: 17 minutes 39.84 seconds (1059.84 seconds total)