Starting phenix.real_space_refine
on Tue Mar  3 15:26:36 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wgc_32483/03_2026/7wgc_32483.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wgc_32483/03_2026/7wgc_32483.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wgc_32483/03_2026/7wgc_32483.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wgc_32483/03_2026/7wgc_32483.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wgc_32483/03_2026/7wgc_32483.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wgc_32483/03_2026/7wgc_32483.cif"
  }
  resolution = 3.6
  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=   0.001 sd=   0.069
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      37      5.16       5
     C    4178      2.51       5
     N    1081      2.21       5
     O    1231      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  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: 6527
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4845
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 594, 4845
          Classifications: {'peptide': 594}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 566}
    Chain: "C"
      Number of atoms: 1612
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1612
          Classifications: {'peptide': 201}
          Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 187}
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.44, per 1000 atoms: 0.22
  Number of scatterers: 6527
  At special positions: 0
  Unit cell: (81.32, 87.74, 120.91, 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      37     16.00
     O    1231      8.00
     N    1081      7.00
     C    4178      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " 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
    NAG-ASN
      " NAG A 701 " - " ASN A 546 "
      " NAG A 702 " - " ASN A  90 "
      " NAG A 703 " - " ASN A 322 "
      " NAG A 704 " - " ASN A  53 "
      " NAG C1301 " - " ASN C 343 "
  Time building additional restraints: 0.62
  Conformation dependent library (CDL) restraints added in 240.4 milliseconds
  

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1502

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 3 sheets defined
      53.8% alpha, 5.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 4.035A  pdb=" N   GLN A  24 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 81
    Processing helix  chain 'A' and resid 91 through 102
      removed outlier: 3.921A  pdb=" N   GLN A 102 " --> pdb=" O   GLN A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 108
      removed outlier: 4.128A  pdb=" N   VAL A 107 " --> pdb=" O   GLY A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 129
    Processing helix  chain 'A' and resid 146 through 153
    Processing helix  chain 'A' and resid 157 through 169
      removed outlier: 3.776A  pdb=" N   ARG A 161 " --> pdb=" O   ASP A 157 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   ARG A 169 " --> pdb=" O   TRP A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 172 through 194
      removed outlier: 3.763A  pdb=" N   LEU A 176 " --> pdb=" O   VAL A 172 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ARG A 177 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
      removed outlier: 3.526A  pdb=" N   ASN A 194 " --> pdb=" O   MET A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 206 through 208
      No H-bonds generated for 'chain 'A' and resid 206 through 208'
    Processing helix  chain 'A' and resid 220 through 252
      removed outlier: 3.911A  pdb=" N   GLU A 224 " --> pdb=" O   GLY A 220 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
    Processing helix  chain 'A' and resid 263 through 268
      removed outlier: 4.225A  pdb=" N   GLY A 268 " --> pdb=" O   HIS A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 282
      removed outlier: 4.418A  pdb=" N   SER A 280 " --> pdb=" O   ASN A 277 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   THR A 282 " --> pdb=" O   TYR A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 300
    Processing helix  chain 'A' and resid 303 through 319
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.502A  pdb=" N   PHE A 327 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   GLU A 329 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   SER A 331 " --> pdb=" O   TRP A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
      removed outlier: 4.065A  pdb=" N   TYR A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 388
      No H-bonds generated for 'chain 'A' and resid 386 through 388'
    Processing helix  chain 'A' and resid 399 through 413
      removed outlier: 3.567A  pdb=" N   ALA A 403 " --> pdb=" O   GLY A 399 " (cutoff:3.500A)
      removed outlier: 5.040A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   SER A 409 " --> pdb=" O   GLY A 405 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ALA A 413 " --> pdb=" O   SER A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 422
    Processing helix  chain 'A' and resid 431 through 447
      removed outlier: 3.709A  pdb=" N   GLU A 435 " --> pdb=" O   ASP A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 465
    Processing helix  chain 'A' and resid 472 through 483
    Processing helix  chain 'A' and resid 498 through 502
    Processing helix  chain 'A' and resid 503 through 508
      removed outlier: 3.548A  pdb=" N   SER A 507 " --> pdb=" O   LEU A 503 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 513 through 532
      removed outlier: 3.732A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ALA A 532 " --> pdb=" O   ALA A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 4.141A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 574
      removed outlier: 3.869A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 588
    Processing helix  chain 'A' and resid 588 through 599
    Processing helix  chain 'C' and resid 339 through 343
      removed outlier: 3.518A  pdb=" N   PHE C 342 " --> pdb=" O   ASP C 339 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 365 through 370
      removed outlier: 3.595A  pdb=" N   TYR C 369 " --> pdb=" O   TYR C 365 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 405 through 408
      removed outlier: 3.566A  pdb=" N   ARG C 408 " --> pdb=" O   ASP C 405 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 405 through 408'
    Processing helix  chain 'C' and resid 438 through 443
      removed outlier: 3.604A  pdb=" N   SER C 443 " --> pdb=" O   ASN C 439 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 347 through 350
    Processing sheet with id=AA2, first strand: chain 'C' and resid 354 through 358
    Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454

    294 hydrogen bonds defined for protein.
    831 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: 0.74

  Time building geometry restraints manager: 0.82 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2090
        1.35 -     1.47: 1743
        1.47 -     1.59: 2820
        1.59 -     1.71: 0
        1.71 -     1.83: 58
  Bond restraints: 6711
  Sorted by residual:
  bond pdb=" C1  NAG A 703 "
       pdb=" O5  NAG A 703 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.39e+00
  bond pdb=" C1  NAG C1301 "
       pdb=" O5  NAG C1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.34e+00
  bond pdb=" C1  NAG A 701 "
       pdb=" O5  NAG A 701 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.91e+00
  bond pdb=" C1  NAG A 704 "
       pdb=" O5  NAG A 704 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.70e+00
  bond pdb=" C1  NAG A 702 "
       pdb=" O5  NAG A 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.431 -0.025 2.00e-02 2.50e+03 1.63e+00
  ... (remaining 6706 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 8930
        1.90 -     3.81: 158
        3.81 -     5.71: 21
        5.71 -     7.61: 8
        7.61 -     9.52: 3
  Bond angle restraints: 9120
  Sorted by residual:
  angle pdb=" C   ASN C 331 "
        pdb=" N   ILE C 332 "
        pdb=" CA  ILE C 332 "
      ideal   model   delta    sigma   weight residual
     121.70  130.63   -8.93 1.80e+00 3.09e-01 2.46e+01
  angle pdb=" C   LEU C 518 "
        pdb=" N   HIS C 519 "
        pdb=" CA  HIS C 519 "
      ideal   model   delta    sigma   weight residual
     122.46  116.19    6.27 1.80e+00 3.09e-01 1.21e+01
  angle pdb=" C   TRP A 461 "
        pdb=" N   MET A 462 "
        pdb=" CA  MET A 462 "
      ideal   model   delta    sigma   weight residual
     121.58  114.86    6.72 1.95e+00 2.63e-01 1.19e+01
  angle pdb=" CA  MET A 462 "
        pdb=" CB  MET A 462 "
        pdb=" CG  MET A 462 "
      ideal   model   delta    sigma   weight residual
     114.10  120.13   -6.03 2.00e+00 2.50e-01 9.08e+00
  angle pdb=" CB  MET A 462 "
        pdb=" CG  MET A 462 "
        pdb=" SD  MET A 462 "
      ideal   model   delta    sigma   weight residual
     112.70  121.69   -8.99 3.00e+00 1.11e-01 8.99e+00
  ... (remaining 9115 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.63: 3570
       17.63 -    35.25: 375
       35.25 -    52.88: 66
       52.88 -    70.51: 16
       70.51 -    88.13: 9
  Dihedral angle restraints: 4036
    sinusoidal: 1699
      harmonic: 2337
  Sorted by residual:
  dihedral pdb=" CB  CYS C 480 "
           pdb=" SG  CYS C 480 "
           pdb=" SG  CYS C 488 "
           pdb=" CB  CYS C 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -154.56   68.56     1      1.00e+01 1.00e-02 6.09e+01
  dihedral pdb=" CB  CYS A 344 "
           pdb=" SG  CYS A 344 "
           pdb=" SG  CYS A 361 "
           pdb=" CB  CYS A 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   25.56   67.44     1      1.00e+01 1.00e-02 5.92e+01
  dihedral pdb=" CA  LEU C 517 "
           pdb=" C   LEU C 517 "
           pdb=" N   LEU C 518 "
           pdb=" CA  LEU C 518 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  147.52   32.48     0      5.00e+00 4.00e-02 4.22e+01
  ... (remaining 4033 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 851
       0.063 -    0.127: 107
       0.127 -    0.190: 8
       0.190 -    0.254: 2
       0.254 -    0.317: 1
  Chirality restraints: 969
  Sorted by residual:
  chirality pdb=" C1  NAG A 703 "
            pdb=" ND2 ASN A 322 "
            pdb=" C2  NAG A 703 "
            pdb=" O5  NAG A 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.08   -0.32 2.00e-01 2.50e+01 2.52e+00
  chirality pdb=" CA  ARG C 355 "
            pdb=" N   ARG C 355 "
            pdb=" C   ARG C 355 "
            pdb=" CB  ARG C 355 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" CB  ILE C 332 "
            pdb=" CA  ILE C 332 "
            pdb=" CG1 ILE C 332 "
            pdb=" CG2 ILE C 332 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.19 2.00e-01 2.50e+01 9.49e-01
  ... (remaining 966 not shown)

  Planarity restraints: 1180
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 478 "    0.029 5.00e-02 4.00e+02   4.37e-02 3.06e+00
        pdb=" N   PRO C 479 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO C 479 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO C 479 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C 383 "    0.021 5.00e-02 4.00e+02   3.17e-02 1.61e+00
        pdb=" N   PRO C 384 "   -0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO C 384 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C 384 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 520 "   -0.019 5.00e-02 4.00e+02   2.96e-02 1.40e+00
        pdb=" N   PRO C 521 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO C 521 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO C 521 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1177 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 382
        2.73 -     3.27: 6821
        3.27 -     3.82: 10569
        3.82 -     4.36: 11942
        4.36 -     4.90: 20366
  Nonbonded interactions: 50080
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 327 "
            pdb=" OG  SER A 331 "
     model   vdw
     2.191 3.040
  nonbonded pdb=" OG  SER A 155 "
            pdb=" OD1 ASP A 157 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" N   SER A  19 "
            pdb=" OD1 ASN C 477 "
     model   vdw
     2.220 3.120
  nonbonded pdb=" OH  TYR A  41 "
            pdb=" OG1 THR C 500 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" O   THR A 125 "
            pdb=" OG1 THR A 129 "
     model   vdw
     2.232 3.040
  ... (remaining 50075 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: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             3.770
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.980
  Find NCS groups from input model:        0.020
  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:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5455
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      :  0.003   0.041   6723  Z= 0.148
  Angle     :  0.644   9.517   9149  Z= 0.331
  Chirality :  0.044   0.317    969
  Planarity :  0.004   0.044   1175
  Dihedral  : 14.721  88.132   2513
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.13 %
    Twisted Proline : 2.56 %
    Twisted General : 0.13 %

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: -0.11 (0.30), residues: 791
  helix:  0.77 (0.27), residues: 384
  sheet:  0.51 (0.65), residues: 48
  loop : -1.06 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 493 
 TYR   0.009   0.001   TYR C 495 
 PHE   0.017   0.001   PHE C 400 
 TRP   0.010   0.001   TRP A 594 
 HIS   0.002   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 6711)
  covalent geometry    : angle       0.63478 ( 9120)
  SS BOND              : bond        0.00174 (    7)
  SS BOND              : angle       0.86538 (   14)
  hydrogen bonds       : bond        0.14036 (  294)
  hydrogen bonds       : angle       4.88236 (  831)
  link_NAG-ASN         : bond        0.00671 (    5)
  link_NAG-ASN         : angle       2.73336 (   15)

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.232 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 88
  average time/residue: 0.0725
  time to fit residues: 8.8229
Evaluate side-chains
  68 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:    0.3980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 519 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4580 r_free = 0.4580 target = 0.210580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.202157 restraints weight = 13753.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.202404 restraints weight = 8733.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.202376 restraints weight = 7993.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.202376 restraints weight = 7321.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.202376 restraints weight = 7321.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.4498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5497
moved from start:          0.1117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   6723  Z= 0.163
  Angle     :  0.643   9.115   9149  Z= 0.330
  Chirality :  0.045   0.357    969
  Planarity :  0.004   0.044   1175
  Dihedral  :  6.001  41.651    969
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  8.42 %
    Favored  : 90.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.13 %
    Twisted Proline : 2.56 %
    Twisted General : 0.27 %

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: -0.13 (0.30), residues: 791
  helix:  0.72 (0.27), residues: 382
  sheet:  0.66 (0.64), residues: 51
  loop : -1.07 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 493 
 TYR   0.014   0.001   TYR A 516 
 PHE   0.030   0.002   PHE A 438 
 TRP   0.008   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 6711)
  covalent geometry    : angle       0.63316 ( 9120)
  SS BOND              : bond        0.00165 (    7)
  SS BOND              : angle       0.80868 (   14)
  hydrogen bonds       : bond        0.04917 (  294)
  hydrogen bonds       : angle       4.31114 (  831)
  link_NAG-ASN         : bond        0.00668 (    5)
  link_NAG-ASN         : angle       2.81446 (   15)

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 76
  time to evaluate  : 0.167 
Fit side-chains
REVERT: A  454 TYR cc_start: 0.7738 (t80) cc_final: 0.7138 (t80)
REVERT: C  406 GLU cc_start: 0.7266 (mp0) cc_final: 0.6860 (mp0)
REVERT: C  448 ASN cc_start: 0.7766 (t0) cc_final: 0.7463 (t0)
  outliers start: 5
  outliers final: 5
  residues processed: 77
  average time/residue: 0.0759
  time to fit residues: 8.1605
Evaluate side-chains
  73 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  498 CYS
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  581 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 58 optimal weight:    9.9990
   chunk 2 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   chunk 32 optimal weight:    0.0870
   chunk 55 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 4 optimal weight:    7.9990
   overall best weight:    1.9964

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

Flipped N/Q/H residues before XYZ refinement:
** A  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4550 r_free = 0.4550 target = 0.207364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4460 r_free = 0.4460 target = 0.198615 restraints weight = 13462.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.198640 restraints weight = 8294.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.198639 restraints weight = 8159.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.198657 restraints weight = 7413.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.198658 restraints weight = 7728.765|
|-----------------------------------------------------------------------------|
r_work (final): 0.4459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5616
moved from start:          0.1899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.095   6723  Z= 0.252
  Angle     :  0.772  17.416   9149  Z= 0.391
  Chirality :  0.050   0.371    969
  Planarity :  0.005   0.049   1175
  Dihedral  :  6.836  49.712    969
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 10.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 13.12 %
    Favored  : 85.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.13 %
    Twisted Proline : 2.56 %
    Twisted General : 0.40 %

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: -0.57 (0.29), residues: 791
  helix:  0.46 (0.27), residues: 381
  sheet:  0.41 (0.67), residues: 48
  loop : -1.39 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 355 
 TYR   0.021   0.002   TYR C 453 
 PHE   0.031   0.002   PHE A 438 
 TRP   0.009   0.001   TRP A 165 
 HIS   0.006   0.001   HIS A 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00580 ( 6711)
  covalent geometry    : angle       0.76254 ( 9120)
  SS BOND              : bond        0.00268 (    7)
  SS BOND              : angle       1.36734 (   14)
  hydrogen bonds       : bond        0.06027 (  294)
  hydrogen bonds       : angle       4.55916 (  831)
  link_NAG-ASN         : bond        0.00642 (    5)
  link_NAG-ASN         : angle       2.91183 (   15)

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.193 
Fit side-chains
REVERT: A  123 MET cc_start: 0.4841 (mmm) cc_final: 0.4561 (mmp)
REVERT: A  376 MET cc_start: 0.7754 (tpt) cc_final: 0.7551 (tpt)
REVERT: A  408 MET cc_start: 0.8366 (mpp) cc_final: 0.7909 (mpp)
REVERT: A  454 TYR cc_start: 0.7893 (t80) cc_final: 0.7155 (t80)
REVERT: A  526 GLN cc_start: 0.7107 (tp40) cc_final: 0.6226 (tp40)
REVERT: C  448 ASN cc_start: 0.7676 (t0) cc_final: 0.7333 (t0)
  outliers start: 11
  outliers final: 9
  residues processed: 72
  average time/residue: 0.0721
  time to fit residues: 7.1331
Evaluate side-chains
  73 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  498 CYS
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  405 ASP
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain C residue  469 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 18 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 59 optimal weight:    0.5980
   chunk 6 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
** A  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  60 GLN
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4564 r_free = 0.4564 target = 0.209241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4487 r_free = 0.4487 target = 0.201578 restraints weight = 13600.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.202611 restraints weight = 8051.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4493 r_free = 0.4493 target = 0.202015 restraints weight = 5290.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4492 r_free = 0.4492 target = 0.201984 restraints weight = 4854.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4493 r_free = 0.4493 target = 0.202040 restraints weight = 4148.375|
|-----------------------------------------------------------------------------|
r_work (final): 0.4495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5528
moved from start:          0.1825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   6723  Z= 0.161
  Angle     :  0.651  11.650   9149  Z= 0.328
  Chirality :  0.045   0.363    969
  Planarity :  0.004   0.050   1175
  Dihedral  :  6.192  44.593    969
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 14.41 %
    Favored  : 83.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.13 %
    Twisted Proline : 2.56 %
    Twisted General : 0.27 %

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: -0.42 (0.30), residues: 791
  helix:  0.58 (0.27), residues: 381
  sheet:  0.47 (0.67), residues: 48
  loop : -1.32 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 355 
 TYR   0.014   0.001   TYR C 369 
 PHE   0.029   0.002   PHE A 438 
 TRP   0.010   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 6711)
  covalent geometry    : angle       0.64058 ( 9120)
  SS BOND              : bond        0.00156 (    7)
  SS BOND              : angle       0.95272 (   14)
  hydrogen bonds       : bond        0.05011 (  294)
  hydrogen bonds       : angle       4.29735 (  831)
  link_NAG-ASN         : bond        0.00678 (    5)
  link_NAG-ASN         : angle       2.83642 (   15)

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.243 
Fit side-chains
REVERT: A  190 MET cc_start: 0.7125 (tpt) cc_final: 0.6895 (tpt)
REVERT: A  454 TYR cc_start: 0.7797 (t80) cc_final: 0.7062 (t80)
REVERT: C  448 ASN cc_start: 0.7643 (t0) cc_final: 0.7309 (t0)
  outliers start: 16
  outliers final: 9
  residues processed: 80
  average time/residue: 0.0677
  time to fit residues: 7.7522
Evaluate side-chains
  72 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  498 CYS
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain C residue  517 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 24 optimal weight:    8.9990
   chunk 39 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   chunk 69 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
** A  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4565 r_free = 0.4565 target = 0.209098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4467 r_free = 0.4467 target = 0.199697 restraints weight = 13517.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4490 r_free = 0.4490 target = 0.201709 restraints weight = 11426.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.202050 restraints weight = 4707.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.202419 restraints weight = 3995.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.202658 restraints weight = 3034.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.4502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5533
moved from start:          0.2005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   6723  Z= 0.168
  Angle     :  0.650   9.301   9149  Z= 0.331
  Chirality :  0.045   0.360    969
  Planarity :  0.004   0.050   1175
  Dihedral  :  6.185  45.181    969
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 16.26 %
    Favored  : 81.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.13 %
    Twisted Proline : 2.56 %
    Twisted General : 0.27 %

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: -0.42 (0.30), residues: 791
  helix:  0.57 (0.27), residues: 381
  sheet:  0.45 (0.67), residues: 48
  loop : -1.29 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 355 
 TYR   0.015   0.001   TYR C 369 
 PHE   0.029   0.002   PHE A 438 
 TRP   0.009   0.001   TRP A 165 
 HIS   0.004   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 6711)
  covalent geometry    : angle       0.63968 ( 9120)
  SS BOND              : bond        0.00130 (    7)
  SS BOND              : angle       0.83626 (   14)
  hydrogen bonds       : bond        0.05017 (  294)
  hydrogen bonds       : angle       4.28431 (  831)
  link_NAG-ASN         : bond        0.00669 (    5)
  link_NAG-ASN         : angle       2.82175 (   15)

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 63
  time to evaluate  : 0.286 
Fit side-chains
REVERT: A  190 MET cc_start: 0.7286 (tpt) cc_final: 0.7070 (tpt)
REVERT: A  408 MET cc_start: 0.8288 (mpp) cc_final: 0.7991 (mpp)
REVERT: A  454 TYR cc_start: 0.7740 (t80) cc_final: 0.7049 (t80)
REVERT: C  448 ASN cc_start: 0.7694 (t0) cc_final: 0.7339 (t0)
  outliers start: 19
  outliers final: 12
  residues processed: 78
  average time/residue: 0.0623
  time to fit residues: 7.0367
Evaluate side-chains
  73 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  407 ILE
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  498 CYS
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain C residue  517 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 78 optimal weight:    0.7980
   chunk 39 optimal weight:    6.9990
   chunk 47 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 27 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   chunk 13 optimal weight:    6.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4578 r_free = 0.4578 target = 0.210312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4488 r_free = 0.4488 target = 0.201546 restraints weight = 13867.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4489 r_free = 0.4489 target = 0.201566 restraints weight = 8907.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4489 r_free = 0.4489 target = 0.201566 restraints weight = 9189.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4489 r_free = 0.4489 target = 0.201566 restraints weight = 9011.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4489 r_free = 0.4489 target = 0.201592 restraints weight = 8217.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.4487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5535
moved from start:          0.2032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6723  Z= 0.139
  Angle     :  0.610   9.082   9149  Z= 0.310
  Chirality :  0.044   0.355    969
  Planarity :  0.004   0.049   1175
  Dihedral  :  5.863  42.887    969
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 17.12 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.13 %
    Twisted Proline : 2.56 %
    Twisted General : 0.13 %

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: -0.28 (0.30), residues: 791
  helix:  0.68 (0.27), residues: 381
  sheet: -0.00 (0.67), residues: 53
  loop : -1.15 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 355 
 TYR   0.013   0.001   TYR C 369 
 PHE   0.028   0.002   PHE A 438 
 TRP   0.008   0.001   TRP A 165 
 HIS   0.002   0.001   HIS A 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 6711)
  covalent geometry    : angle       0.59977 ( 9120)
  SS BOND              : bond        0.00136 (    7)
  SS BOND              : angle       0.76005 (   14)
  hydrogen bonds       : bond        0.04611 (  294)
  hydrogen bonds       : angle       4.18498 (  831)
  link_NAG-ASN         : bond        0.00673 (    5)
  link_NAG-ASN         : angle       2.78207 (   15)

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 0.237 
Fit side-chains
REVERT: A  408 MET cc_start: 0.8350 (mpp) cc_final: 0.7922 (mpp)
REVERT: A  454 TYR cc_start: 0.7767 (t80) cc_final: 0.7037 (t80)
REVERT: C  448 ASN cc_start: 0.7659 (t0) cc_final: 0.7314 (t0)
  outliers start: 16
  outliers final: 11
  residues processed: 76
  average time/residue: 0.0746
  time to fit residues: 7.9107
Evaluate side-chains
  72 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  359 SER
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain C residue  517 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 56 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4553 r_free = 0.4553 target = 0.207666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4453 r_free = 0.4453 target = 0.197880 restraints weight = 13190.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4453 r_free = 0.4453 target = 0.197885 restraints weight = 8192.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4453 r_free = 0.4453 target = 0.197884 restraints weight = 8884.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4453 r_free = 0.4453 target = 0.197891 restraints weight = 7658.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4453 r_free = 0.4453 target = 0.197898 restraints weight = 7956.340|
|-----------------------------------------------------------------------------|
r_work (final): 0.4453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5643
moved from start:          0.2329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.081   6723  Z= 0.229
  Angle     :  0.739  11.786   9149  Z= 0.373
  Chirality :  0.047   0.366    969
  Planarity :  0.004   0.051   1175
  Dihedral  :  6.570  49.430    969
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 17.12 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.13 %
    Twisted Proline : 2.56 %
    Twisted General : 0.40 %

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: -0.52 (0.30), residues: 791
  helix:  0.50 (0.27), residues: 380
  sheet:  0.30 (0.66), residues: 48
  loop : -1.35 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 355 
 TYR   0.014   0.002   TYR C 453 
 PHE   0.031   0.002   PHE A 438 
 TRP   0.009   0.001   TRP A 165 
 HIS   0.005   0.001   HIS A 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00527 ( 6711)
  covalent geometry    : angle       0.73044 ( 9120)
  SS BOND              : bond        0.00189 (    7)
  SS BOND              : angle       0.82996 (   14)
  hydrogen bonds       : bond        0.05577 (  294)
  hydrogen bonds       : angle       4.41862 (  831)
  link_NAG-ASN         : bond        0.00667 (    5)
  link_NAG-ASN         : angle       2.87501 (   15)

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 63
  time to evaluate  : 0.236 
Fit side-chains
REVERT: A  408 MET cc_start: 0.8347 (mpp) cc_final: 0.8112 (mpp)
REVERT: A  454 TYR cc_start: 0.7822 (t80) cc_final: 0.7163 (t80)
REVERT: C  448 ASN cc_start: 0.7755 (t0) cc_final: 0.7384 (t0)
  outliers start: 18
  outliers final: 16
  residues processed: 78
  average time/residue: 0.0650
  time to fit residues: 7.2181
Evaluate side-chains
  74 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 58
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  407 ILE
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  359 SER
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain C residue  429 PHE
Chi-restraints excluded: chain C residue  517 LEU
Chi-restraints excluded: chain C residue  528 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 9 optimal weight:    6.9990
   chunk 16 optimal weight:    0.8980
   chunk 35 optimal weight:    6.9990
   chunk 19 optimal weight:    0.8980
   chunk 37 optimal weight:    0.6980
   chunk 45 optimal weight:    7.9990
   chunk 63 optimal weight:    0.9990
   chunk 74 optimal weight:    0.6980
   chunk 40 optimal weight:    0.0770
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 422 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4584 r_free = 0.4584 target = 0.210906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.202162 restraints weight = 13703.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.202182 restraints weight = 8608.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.202180 restraints weight = 8638.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4496 r_free = 0.4496 target = 0.202195 restraints weight = 7685.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4496 r_free = 0.4496 target = 0.202194 restraints weight = 8670.586|
|-----------------------------------------------------------------------------|
r_work (final): 0.4494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5508
moved from start:          0.2207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6723  Z= 0.124
  Angle     :  0.607   9.092   9149  Z= 0.307
  Chirality :  0.043   0.361    969
  Planarity :  0.004   0.050   1175
  Dihedral  :  5.626  40.829    969
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 18.26 %
    Favored  : 79.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.13 %
    Twisted Proline : 2.56 %
    Twisted General : 0.13 %

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: -0.27 (0.30), residues: 791
  helix:  0.70 (0.27), residues: 381
  sheet:  0.05 (0.66), residues: 51
  loop : -1.16 (0.33), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 355 
 TYR   0.011   0.001   TYR C 369 
 PHE   0.028   0.002   PHE A 438 
 TRP   0.008   0.001   TRP A 165 
 HIS   0.002   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 6711)
  covalent geometry    : angle       0.59684 ( 9120)
  SS BOND              : bond        0.00204 (    7)
  SS BOND              : angle       0.74794 (   14)
  hydrogen bonds       : bond        0.04329 (  294)
  hydrogen bonds       : angle       4.15522 (  831)
  link_NAG-ASN         : bond        0.00692 (    5)
  link_NAG-ASN         : angle       2.80375 (   15)

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 66
  time to evaluate  : 0.177 
Fit side-chains
REVERT: A  454 TYR cc_start: 0.7837 (t80) cc_final: 0.7043 (t80)
REVERT: C  448 ASN cc_start: 0.7647 (t0) cc_final: 0.7318 (t0)
  outliers start: 16
  outliers final: 12
  residues processed: 79
  average time/residue: 0.0607
  time to fit residues: 6.9871
Evaluate side-chains
  73 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  327 PHE
Chi-restraints excluded: chain A residue  407 ILE
Chi-restraints excluded: chain A residue  411 SER
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  359 SER
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain C residue  429 PHE
Chi-restraints excluded: chain C residue  525 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 39 optimal weight:    0.4980
   chunk 77 optimal weight:    0.9990
   chunk 55 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 60 optimal weight:    0.7980
   chunk 51 optimal weight:    0.0170
   chunk 78 optimal weight:    0.0770
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.3976

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

Flipped N/Q/H residues before XYZ refinement:
** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4598 r_free = 0.4598 target = 0.212769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4510 r_free = 0.4510 target = 0.204059 restraints weight = 13692.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.204135 restraints weight = 8312.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.204080 restraints weight = 8438.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.204089 restraints weight = 7322.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.204087 restraints weight = 8296.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.4512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5455
moved from start:          0.2217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6723  Z= 0.115
  Angle     :  0.612   9.009   9149  Z= 0.304
  Chirality :  0.043   0.353    969
  Planarity :  0.004   0.048   1175
  Dihedral  :  5.239  38.251    969
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 19.97 %
    Favored  : 78.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.13 %
    Twisted Proline : 2.56 %
    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: -0.09 (0.30), residues: 791
  helix:  0.85 (0.28), residues: 379
  sheet:  0.12 (0.67), residues: 51
  loop : -1.04 (0.33), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 355 
 TYR   0.016   0.001   TYR C 369 
 PHE   0.029   0.002   PHE A 438 
 TRP   0.007   0.001   TRP A 594 
 HIS   0.004   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 6711)
  covalent geometry    : angle       0.60228 ( 9120)
  SS BOND              : bond        0.00173 (    7)
  SS BOND              : angle       0.65932 (   14)
  hydrogen bonds       : bond        0.04020 (  294)
  hydrogen bonds       : angle       4.03820 (  831)
  link_NAG-ASN         : bond        0.00694 (    5)
  link_NAG-ASN         : angle       2.71672 (   15)

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.240 
Fit side-chains
REVERT: A  454 TYR cc_start: 0.7788 (t80) cc_final: 0.7006 (t80)
REVERT: C  406 GLU cc_start: 0.7507 (mp0) cc_final: 0.7114 (pm20)
REVERT: C  448 ASN cc_start: 0.7534 (t0) cc_final: 0.7217 (t0)
  outliers start: 11
  outliers final: 11
  residues processed: 73
  average time/residue: 0.0694
  time to fit residues: 6.9822
Evaluate side-chains
  73 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  411 SER
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  359 SER
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain C residue  528 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 65 optimal weight:    0.5980
   chunk 17 optimal weight:    0.3980
   chunk 33 optimal weight:    0.9980
   chunk 54 optimal weight:    0.4980
   chunk 29 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 59 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4590 r_free = 0.4590 target = 0.211620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4504 r_free = 0.4504 target = 0.203086 restraints weight = 13793.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.203134 restraints weight = 8765.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.203118 restraints weight = 8820.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.203143 restraints weight = 7053.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.203143 restraints weight = 8442.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.4503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5476
moved from start:          0.2270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6723  Z= 0.124
  Angle     :  0.623   9.030   9149  Z= 0.309
  Chirality :  0.043   0.351    969
  Planarity :  0.004   0.046   1175
  Dihedral  :  5.365  39.123    969
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 19.40 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.13 %
    Twisted Proline : 2.56 %
    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: -0.07 (0.30), residues: 791
  helix:  0.82 (0.28), residues: 380
  sheet:  0.21 (0.68), residues: 51
  loop : -1.00 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 355 
 TYR   0.015   0.001   TYR C 369 
 PHE   0.033   0.002   PHE A 438 
 TRP   0.009   0.001   TRP A 461 
 HIS   0.002   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 6711)
  covalent geometry    : angle       0.61308 ( 9120)
  SS BOND              : bond        0.00133 (    7)
  SS BOND              : angle       0.70528 (   14)
  hydrogen bonds       : bond        0.04129 (  294)
  hydrogen bonds       : angle       4.04942 (  831)
  link_NAG-ASN         : bond        0.00688 (    5)
  link_NAG-ASN         : angle       2.74566 (   15)

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A  327 PHE cc_start: 0.5587 (t80) cc_final: 0.5326 (t80)
REVERT: A  454 TYR cc_start: 0.7801 (t80) cc_final: 0.7035 (t80)
REVERT: C  448 ASN cc_start: 0.7547 (t0) cc_final: 0.7237 (t0)
  outliers start: 12
  outliers final: 11
  residues processed: 74
  average time/residue: 0.0658
  time to fit residues: 6.7339
Evaluate side-chains
  73 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  407 ILE
Chi-restraints excluded: chain A residue  411 SER
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  359 SER
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain C residue  528 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 11 optimal weight:    0.0770
   chunk 40 optimal weight:    0.0770
   chunk 64 optimal weight:    0.0470
   chunk 9 optimal weight:    6.9990
   chunk 27 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0570
   chunk 20 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.2112

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

Flipped N/Q/H residues before XYZ refinement:
** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4622 r_free = 0.4622 target = 0.215146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4537 r_free = 0.4537 target = 0.206616 restraints weight = 13613.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.206696 restraints weight = 7994.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.206681 restraints weight = 7864.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.206692 restraints weight = 6405.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.206716 restraints weight = 5951.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.4536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5391
moved from start:          0.2412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6723  Z= 0.111
  Angle     :  0.612   9.182   9149  Z= 0.303
  Chirality :  0.043   0.357    969
  Planarity :  0.003   0.046   1175
  Dihedral  :  4.826  35.008    969
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 19.54 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.13 %
    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: -0.04 (0.30), residues: 791
  helix:  0.78 (0.28), residues: 390
  sheet:  0.26 (0.69), residues: 51
  loop : -0.95 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 355 
 TYR   0.014   0.001   TYR C 369 
 PHE   0.032   0.001   PHE A 438 
 TRP   0.010   0.001   TRP A 594 
 HIS   0.002   0.000   HIS A 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 6711)
  covalent geometry    : angle       0.60268 ( 9120)
  SS BOND              : bond        0.00201 (    7)
  SS BOND              : angle       0.65423 (   14)
  hydrogen bonds       : bond        0.03680 (  294)
  hydrogen bonds       : angle       3.97163 (  831)
  link_NAG-ASN         : bond        0.00712 (    5)
  link_NAG-ASN         : angle       2.74023 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1065.54 seconds
wall clock time: 19 minutes 8.26 seconds (1148.26 seconds total)