Starting phenix.real_space_refine
on Thu Jul  2 04:17:10 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7wgc_32483/07_2026/7wgc_32483.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wgc_32483/07_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 {
    restraint_files = "/net/cci-nas-00/data/ceres_data/7wgc_32483/07_2026/7wgc_32483.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7wgc_32483/07_2026/7wgc_32483.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wgc_32483/07_2026/7wgc_32483.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wgc_32483/07_2026/7wgc_32483.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wgc_32483/07_2026/7wgc_32483.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wgc_32483/07_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-6108/lib/python3.11/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 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 chiralities: 1
  Time building chain proxies: 1.49, per 1000 atoms: 0.23
  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: 0.55
  Conformation dependent library (CDL) restraints added in 362.1 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: 0.17
  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: 0.89

  Time building geometry restraints manager: 0.80 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 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: 3478
       17.63 -    35.25: 368
       35.25 -    52.88: 60
       52.88 -    70.51: 16
       70.51 -    88.13: 9
  Dihedral angle restraints: 3931
    sinusoidal: 1594
      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 3928 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:             3.150
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.130
  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:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5469
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  : 14.801  88.132   2408
  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/Z
  covalent geometry    : bond        0.00313 /  0.15 ( 6711)
  covalent geometry    : angle       0.63478 /  0.33 ( 9120)
  SS BOND              : bond        0.00174 /  0.10 (    7)
  SS BOND              : angle       0.86538 /  0.47 (   14)
  hydrogen bonds       : bond        0.14036 /  9.02 (  294)
  hydrogen bonds       : angle       4.88236 /  3.48 (  831)
  link_NAG-ASN         : bond        0.00671 /  0.35 (    5)
  link_NAG-ASN         : angle       2.73336 /  1.66 (   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  : 0.247 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 88
  average time/residue: 0.0662
  time to fit residues: 8.2131
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  : 0.163 
-------------------------------------------------------------------------------
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...
** 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 = 0.4581 r_free = 0.4581 target = 0.210634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.202078 restraints weight = 13770.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.202202 restraints weight = 8733.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.202200 restraints weight = 8772.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.201546 restraints weight = 7197.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4488 r_free = 0.4488 target = 0.201331 restraints weight = 7663.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.4490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5579
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= 0.162
  Angle     :  0.643   9.123   9149  Z= 0.329
  Chirality :  0.045   0.356    969
  Planarity :  0.004   0.044   1175
  Dihedral  :  5.479  39.766    864
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  8.27 %
    Favored  : 91.01 %
  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:  0.73 (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   0.005   0.001   ARG C 493 
 TYR   0.014   0.001   TYR A 516 
 PHE   0.029   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/Z
  covalent geometry    : bond        0.00370 /  0.16 ( 6711)
  covalent geometry    : angle       0.63339 /  0.33 ( 9120)
  SS BOND              : bond        0.00163 /  0.08 (    7)
  SS BOND              : angle       0.81449 /  0.44 (   14)
  hydrogen bonds       : bond        0.04948 /  3.48 (  294)
  hydrogen bonds       : angle       4.31026 /  3.10 (  831)
  link_NAG-ASN         : bond        0.00676 /  0.36 (    5)
  link_NAG-ASN         : angle       2.76712 /  1.64 (   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  : 0.235 
Fit side-chains
REVERT: A  454 TYR cc_start: 0.7722 (t80) cc_final: 0.7119 (t80)
REVERT: C  406 GLU cc_start: 0.7239 (mp0) cc_final: 0.6847 (mp0)
REVERT: C  448 ASN cc_start: 0.7741 (t0) cc_final: 0.7445 (t0)
  outliers start: 5
  outliers final: 5
  residues processed: 77
  average time/residue: 0.0648
  time to fit residues: 7.0287
Evaluate side-chains
  72 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 13 optimal weight:    4.9990
   chunk 58 optimal weight:    8.9990
   chunk 2 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.4980
   chunk 32 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 22 optimal weight:    0.5980
   chunk 4 optimal weight:    7.9990
   overall best weight:    1.1784

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4571 r_free = 0.4571 target = 0.209645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4496 r_free = 0.4496 target = 0.202228 restraints weight = 13604.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.203139 restraints weight = 9236.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4502 r_free = 0.4502 target = 0.202766 restraints weight = 5497.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4500 r_free = 0.4500 target = 0.202547 restraints weight = 4369.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4500 r_free = 0.4500 target = 0.202590 restraints weight = 3612.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.4500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5509
moved from start:          0.1436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   6723  Z= 0.167
  Angle     :  0.649  12.096   9149  Z= 0.329
  Chirality :  0.045   0.364    969
  Planarity :  0.004   0.045   1175
  Dihedral  :  5.568  41.733    864
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 12.55 %
    Favored  : 86.16 %
  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: -0.19 (0.30), residues: 791
  helix:  0.72 (0.27), residues: 381
  sheet:  0.61 (0.67), residues: 51
  loop : -1.14 (0.33), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 355 
 TYR   0.014   0.001   TYR C 369 
 PHE   0.030   0.002   PHE A 438 
 TRP   0.008   0.001   TRP A 165 
 HIS   0.004   0.001   HIS A 345 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00380 /  0.17 ( 6711)
  covalent geometry    : angle       0.63889 /  0.33 ( 9120)
  SS BOND              : bond        0.00163 /  0.09 (    7)
  SS BOND              : angle       1.09022 /  0.54 (   14)
  hydrogen bonds       : bond        0.04957 /  3.49 (  294)
  hydrogen bonds       : angle       4.23855 /  3.05 (  831)
  link_NAG-ASN         : bond        0.00665 /  0.36 (    5)
  link_NAG-ASN         : angle       2.79491 /  1.65 (   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
  75 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A  123 MET cc_start: 0.5668 (mmm) cc_final: 0.5337 (mmp)
REVERT: A  408 MET cc_start: 0.8155 (mpp) cc_final: 0.7856 (mpp)
REVERT: A  454 TYR cc_start: 0.7765 (t80) cc_final: 0.7080 (t80)
REVERT: C  405 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.7409 (p0)
REVERT: C  448 ASN cc_start: 0.7571 (t0) cc_final: 0.7267 (t0)
  outliers start: 9
  outliers final: 5
  residues processed: 71
  average time/residue: 0.0682
  time to fit residues: 6.8431
Evaluate side-chains
  68 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
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  581 VAL
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  405 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 8 optimal weight:    5.9990
   chunk 54 optimal weight:    1.9990
   chunk 35 optimal weight:    6.9990
   chunk 59 optimal weight:    0.6980
   chunk 6 optimal weight:    3.9990
   chunk 69 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   chunk 64 optimal weight:    0.2980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   overall best weight:    1.1984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.4569 r_free = 0.4569 target = 0.209426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4493 r_free = 0.4493 target = 0.201935 restraints weight = 13807.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4500 r_free = 0.4500 target = 0.202641 restraints weight = 8737.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.202211 restraints weight = 5922.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4496 r_free = 0.4496 target = 0.202157 restraints weight = 5551.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4496 r_free = 0.4496 target = 0.202186 restraints weight = 4785.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.4495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5517
moved from start:          0.1639

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= 0.168
  Angle     :  0.649  12.689   9149  Z= 0.327
  Chirality :  0.045   0.365    969
  Planarity :  0.004   0.046   1175
  Dihedral  :  5.577  42.393    864
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 14.41 %
    Favored  : 84.02 %
  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: -0.20 (0.30), residues: 791
  helix:  0.77 (0.27), residues: 375
  sheet:  0.55 (0.68), residues: 51
  loop : -1.19 (0.32), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 355 
 TYR   0.014   0.001   TYR C 453 
 PHE   0.028   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/Z
  covalent geometry    : bond        0.00383 /  0.17 ( 6711)
  covalent geometry    : angle       0.63886 /  0.32 ( 9120)
  SS BOND              : bond        0.00146 /  0.07 (    7)
  SS BOND              : angle       0.91274 /  0.47 (   14)
  hydrogen bonds       : bond        0.04903 /  3.47 (  294)
  hydrogen bonds       : angle       4.19252 /  3.01 (  831)
  link_NAG-ASN         : bond        0.00659 /  0.36 (    5)
  link_NAG-ASN         : angle       2.78429 /  1.65 (   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
  77 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.248 
Fit side-chains
REVERT: A  190 MET cc_start: 0.7236 (tpt) cc_final: 0.6930 (tpt)
REVERT: A  454 TYR cc_start: 0.7850 (t80) cc_final: 0.7142 (t80)
REVERT: C  448 ASN cc_start: 0.7603 (t0) cc_final: 0.7275 (t0)
  outliers start: 11
  outliers final: 7
  residues processed: 73
  average time/residue: 0.0701
  time to fit residues: 7.1558
Evaluate side-chains
  69 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 39 optimal weight:    0.3980
   chunk 71 optimal weight:    0.7980
   chunk 66 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9980
   chunk 20 optimal weight:    0.4980
   chunk 26 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 35 optimal weight:    5.9990
   chunk 15 optimal weight:    2.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  24 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 = 0.4582 r_free = 0.4582 target = 0.210827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.202428 restraints weight = 13991.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.202472 restraints weight = 8787.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.202472 restraints weight = 7765.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.202472 restraints weight = 7765.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.202472 restraints weight = 7765.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.4497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5497
moved from start:          0.1713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6723  Z= 0.127
  Angle     :  0.587   8.972   9149  Z= 0.300
  Chirality :  0.044   0.360    969
  Planarity :  0.004   0.045   1175
  Dihedral  :  5.255  38.894    864
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 15.26 %
    Favored  : 82.88 %
  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: -0.04 (0.30), residues: 791
  helix:  0.87 (0.28), residues: 375
  sheet:  0.64 (0.68), residues: 51
  loop : -1.06 (0.32), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 355 
 TYR   0.010   0.001   TYR A 516 
 PHE   0.026   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/Z
  covalent geometry    : bond        0.00282 /  0.13 ( 6711)
  covalent geometry    : angle       0.57694 /  0.30 ( 9120)
  SS BOND              : bond        0.00152 /  0.09 (    7)
  SS BOND              : angle       0.78871 /  0.42 (   14)
  hydrogen bonds       : bond        0.04394 /  3.11 (  294)
  hydrogen bonds       : angle       4.07776 /  2.94 (  831)
  link_NAG-ASN         : bond        0.00676 /  0.36 (    5)
  link_NAG-ASN         : angle       2.72074 /  1.63 (   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
  79 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.162 
Fit side-chains
REVERT: A  190 MET cc_start: 0.7056 (tpt) cc_final: 0.6853 (tpt)
REVERT: A  408 MET cc_start: 0.8291 (mpp) cc_final: 0.7997 (mpp)
REVERT: A  454 TYR cc_start: 0.7808 (t80) cc_final: 0.7037 (t80)
REVERT: C  448 ASN cc_start: 0.7570 (t0) cc_final: 0.7238 (t0)
  outliers start: 13
  outliers final: 7
  residues processed: 76
  average time/residue: 0.0491
  time to fit residues: 5.4597
Evaluate side-chains
  69 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
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  581 VAL
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  469 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 78 optimal weight:    0.0570
   chunk 39 optimal weight:    0.9990
   chunk 47 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   chunk 27 optimal weight:    0.8980
   chunk 12 optimal weight:    6.9990
   chunk 43 optimal weight:    0.6980
   chunk 13 optimal weight:    5.9990
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.5498

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4591 r_free = 0.4591 target = 0.211598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4507 r_free = 0.4507 target = 0.203343 restraints weight = 14101.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.203401 restraints weight = 8614.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.203387 restraints weight = 8935.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.203408 restraints weight = 7589.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.203413 restraints weight = 8264.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.4504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5473
moved from start:          0.1799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6723  Z= 0.117
  Angle     :  0.572   8.906   9149  Z= 0.291
  Chirality :  0.043   0.352    969
  Planarity :  0.003   0.044   1175
  Dihedral  :  5.032  35.445    864
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 16.69 %
    Favored  : 82.17 %
  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:  0.04 (0.30), residues: 791
  helix:  0.92 (0.28), residues: 375
  sheet:  0.23 (0.67), residues: 56
  loop : -0.94 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 355 
 TYR   0.009   0.001   TYR A 516 
 PHE   0.024   0.001   PHE A 438 
 TRP   0.007   0.001   TRP A 165 
 HIS   0.002   0.001   HIS C 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00257 /  0.12 ( 6711)
  covalent geometry    : angle       0.56216 /  0.29 ( 9120)
  SS BOND              : bond        0.00146 /  0.08 (    7)
  SS BOND              : angle       0.67006 /  0.36 (   14)
  hydrogen bonds       : bond        0.04137 /  2.92 (  294)
  hydrogen bonds       : angle       3.99233 /  2.87 (  831)
  link_NAG-ASN         : bond        0.00678 /  0.35 (    5)
  link_NAG-ASN         : angle       2.67287 /  1.60 (   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
  72 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.236 
Fit side-chains
REVERT: A  408 MET cc_start: 0.8244 (mpp) cc_final: 0.7967 (mpp)
REVERT: A  454 TYR cc_start: 0.7745 (t80) cc_final: 0.6973 (t80)
REVERT: C  448 ASN cc_start: 0.7576 (t0) cc_final: 0.7250 (t0)
  outliers start: 8
  outliers final: 6
  residues processed: 70
  average time/residue: 0.0655
  time to fit residues: 6.5570
Evaluate side-chains
  69 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 63
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   chunk 32 optimal weight:    0.3980
   chunk 56 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 33 optimal weight:    7.9990
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4587 r_free = 0.4587 target = 0.211081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.202629 restraints weight = 13725.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.202683 restraints weight = 8750.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.202657 restraints weight = 9048.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.202670 restraints weight = 7759.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.202669 restraints weight = 8183.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.4498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5499
moved from start:          0.1917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6723  Z= 0.130
  Angle     :  0.604   9.853   9149  Z= 0.303
  Chirality :  0.043   0.356    969
  Planarity :  0.004   0.043   1175
  Dihedral  :  5.072  38.212    864
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 16.69 %
    Favored  : 81.31 %
  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:  0.02 (0.30), residues: 791
  helix:  0.91 (0.28), residues: 374
  sheet:  0.20 (0.66), residues: 56
  loop : -0.94 (0.33), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 355 
 TYR   0.009   0.001   TYR A 516 
 PHE   0.027   0.001   PHE A 438 
 TRP   0.008   0.001   TRP A 165 
 HIS   0.002   0.001   HIS C 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00290 /  0.13 ( 6711)
  covalent geometry    : angle       0.59422 /  0.30 ( 9120)
  SS BOND              : bond        0.00124 /  0.07 (    7)
  SS BOND              : angle       0.67421 /  0.36 (   14)
  hydrogen bonds       : bond        0.04248 /  3.01 (  294)
  hydrogen bonds       : angle       3.98018 /  2.86 (  831)
  link_NAG-ASN         : bond        0.00674 /  0.36 (    5)
  link_NAG-ASN         : angle       2.69464 /  1.62 (   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
  80 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 66
  time to evaluate  : 0.262 
Fit side-chains
REVERT: A  454 TYR cc_start: 0.7738 (t80) cc_final: 0.7231 (t80)
REVERT: C  448 ASN cc_start: 0.7594 (t0) cc_final: 0.7267 (t0)
  outliers start: 14
  outliers final: 9
  residues processed: 78
  average time/residue: 0.0681
  time to fit residues: 7.6474
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  : 0.248 
-------------------------------------------------------------------------------
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  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  525 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 9 optimal weight:    7.9990
   chunk 16 optimal weight:    0.7980
   chunk 35 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.4584 r_free = 0.4584 target = 0.210899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.202119 restraints weight = 13756.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.202149 restraints weight = 9183.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.202141 restraints weight = 9357.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.202154 restraints weight = 8137.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.202155 restraints weight = 9203.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.4495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5513
moved from start:          0.1996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6723  Z= 0.140
  Angle     :  0.622   8.990   9149  Z= 0.312
  Chirality :  0.044   0.361    969
  Planarity :  0.004   0.043   1175
  Dihedral  :  5.190  40.299    864
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 17.55 %
    Favored  : 80.74 %
  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: -0.05 (0.30), residues: 791
  helix:  0.82 (0.27), residues: 380
  sheet:  0.12 (0.66), residues: 56
  loop : -0.96 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 355 
 TYR   0.010   0.001   TYR A 516 
 PHE   0.030   0.002   PHE A 438 
 TRP   0.008   0.001   TRP A 165 
 HIS   0.004   0.001   HIS A 239 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00315 /  0.14 ( 6711)
  covalent geometry    : angle       0.61224 /  0.31 ( 9120)
  SS BOND              : bond        0.00132 /  0.07 (    7)
  SS BOND              : angle       0.69192 /  0.38 (   14)
  hydrogen bonds       : bond        0.04389 /  3.11 (  294)
  hydrogen bonds       : angle       4.01481 /  2.88 (  831)
  link_NAG-ASN         : bond        0.00675 /  0.36 (    5)
  link_NAG-ASN         : angle       2.73717 /  1.64 (   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
  74 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.261 
Fit side-chains
REVERT: A  408 MET cc_start: 0.8240 (mpp) cc_final: 0.7981 (mpp)
REVERT: A  454 TYR cc_start: 0.7839 (t80) cc_final: 0.7050 (t80)
REVERT: C  448 ASN cc_start: 0.7610 (t0) cc_final: 0.7282 (t0)
  outliers start: 12
  outliers final: 9
  residues processed: 72
  average time/residue: 0.0610
  time to fit residues: 6.3593
Evaluate side-chains
  71 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
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  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  525 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 37 optimal weight:    0.0970
   chunk 57 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 77 optimal weight:    0.8980
   chunk 55 optimal weight:    0.0970
   chunk 26 optimal weight:    1.9990
   chunk 60 optimal weight:    0.6980
   chunk 51 optimal weight:    0.2980
   chunk 78 optimal weight:    0.3980
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.3176

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.4612 r_free = 0.4612 target = 0.213986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4527 r_free = 0.4527 target = 0.205519 restraints weight = 13989.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.4528 r_free = 0.4528 target = 0.205599 restraints weight = 8450.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4528 r_free = 0.4528 target = 0.205635 restraints weight = 7385.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4528 r_free = 0.4528 target = 0.205628 restraints weight = 8516.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4529 r_free = 0.4529 target = 0.205643 restraints weight = 6430.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.4528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5412
moved from start:          0.2122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6723  Z= 0.110
  Angle     :  0.597   8.919   9149  Z= 0.298
  Chirality :  0.042   0.353    969
  Planarity :  0.003   0.044   1175
  Dihedral  :  4.639  24.992    864
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 18.40 %
    Favored  : 80.60 %
  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:  0.10 (0.30), residues: 791
  helix:  0.90 (0.28), residues: 382
  sheet:  0.14 (0.65), residues: 56
  loop : -0.82 (0.33), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 493 
 TYR   0.008   0.001   TYR A 516 
 PHE   0.031   0.001   PHE A 438 
 TRP   0.009   0.001   TRP A 594 
 HIS   0.003   0.001   HIS A 239 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00238 /  0.11 ( 6711)
  covalent geometry    : angle       0.58749 /  0.30 ( 9120)
  SS BOND              : bond        0.00192 /  0.13 (    7)
  SS BOND              : angle       0.66472 /  0.37 (   14)
  hydrogen bonds       : bond        0.03737 /  2.62 (  294)
  hydrogen bonds       : angle       3.90650 /  2.80 (  831)
  link_NAG-ASN         : bond        0.00693 /  0.36 (    5)
  link_NAG-ASN         : angle       2.66616 /  1.62 (   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
  81 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 0.259 
Fit side-chains
REVERT: A  408 MET cc_start: 0.8236 (mpp) cc_final: 0.7996 (mpp)
REVERT: A  454 TYR cc_start: 0.7647 (t80) cc_final: 0.6846 (t80)
REVERT: C  448 ASN cc_start: 0.7727 (t0) cc_final: 0.7384 (t0)
  outliers start: 7
  outliers final: 5
  residues processed: 78
  average time/residue: 0.0758
  time to fit residues: 8.2441
Evaluate side-chains
  72 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  525 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 65 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 59 optimal weight:    0.7980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.4591 r_free = 0.4591 target = 0.211540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.202441 restraints weight = 13696.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.202469 restraints weight = 8981.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.202465 restraints weight = 8956.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4500 r_free = 0.4500 target = 0.202511 restraints weight = 7667.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4500 r_free = 0.4500 target = 0.202509 restraints weight = 7942.348|
|-----------------------------------------------------------------------------|
r_work (final): 0.4497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5510
moved from start:          0.2142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6723  Z= 0.138
  Angle     :  0.638   9.080   9149  Z= 0.319
  Chirality :  0.043   0.356    969
  Planarity :  0.004   0.041   1175
  Dihedral  :  4.973  38.204    864
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 18.26 %
    Favored  : 80.88 %
  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:  0.12 (0.31), residues: 791
  helix:  0.92 (0.28), residues: 380
  sheet:  0.38 (0.66), residues: 54
  loop : -0.85 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 355 
 TYR   0.011   0.001   TYR A 381 
 PHE   0.032   0.002   PHE A 438 
 TRP   0.007   0.001   TRP A 461 
 HIS   0.003   0.001   HIS A 239 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.14 ( 6711)
  covalent geometry    : angle       0.62900 /  0.32 ( 9120)
  SS BOND              : bond        0.00127 /  0.06 (    7)
  SS BOND              : angle       0.69753 /  0.37 (   14)
  hydrogen bonds       : bond        0.04255 /  2.99 (  294)
  hydrogen bonds       : angle       3.99526 /  2.87 (  831)
  link_NAG-ASN         : bond        0.00670 /  0.35 (    5)
  link_NAG-ASN         : angle       2.73000 /  1.64 (   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
  74 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 68
  time to evaluate  : 0.149 
Fit side-chains
REVERT: A  408 MET cc_start: 0.8307 (mpp) cc_final: 0.8033 (mpp)
REVERT: A  454 TYR cc_start: 0.7777 (t80) cc_final: 0.6966 (t80)
REVERT: C  406 GLU cc_start: 0.7526 (mp0) cc_final: 0.7149 (pm20)
REVERT: C  448 ASN cc_start: 0.7601 (t0) cc_final: 0.7266 (t0)
  outliers start: 6
  outliers final: 5
  residues processed: 72
  average time/residue: 0.0700
  time to fit residues: 7.0937
Evaluate side-chains
  67 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  525 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   chunk 9 optimal weight:    6.9990
   chunk 27 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9980
   chunk 14 optimal weight:    9.9990
   chunk 58 optimal weight:    0.0870
   chunk 20 optimal weight:    0.7980
   chunk 1 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.6558

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.4592 r_free = 0.4592 target = 0.211890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4500 r_free = 0.4500 target = 0.202812 restraints weight = 13710.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.202843 restraints weight = 9011.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.202844 restraints weight = 9104.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.202864 restraints weight = 7543.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.202866 restraints weight = 9055.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.4499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5488
moved from start:          0.2181

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= 0.128
  Angle     :  0.634   9.071   9149  Z= 0.315
  Chirality :  0.043   0.355    969
  Planarity :  0.004   0.042   1175
  Dihedral  :  4.932  35.614    864
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 18.83 %
    Favored  : 80.31 %
  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:  0.12 (0.30), residues: 791
  helix:  0.90 (0.28), residues: 380
  sheet:  0.40 (0.66), residues: 54
  loop : -0.82 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 355 
 TYR   0.010   0.001   TYR A 516 
 PHE   0.033   0.002   PHE A 438 
 TRP   0.007   0.001   TRP A 461 
 HIS   0.003   0.001   HIS C 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.13 ( 6711)
  covalent geometry    : angle       0.62467 /  0.31 ( 9120)
  SS BOND              : bond        0.00131 /  0.08 (    7)
  SS BOND              : angle       0.69428 /  0.37 (   14)
  hydrogen bonds       : bond        0.04134 /  2.91 (  294)
  hydrogen bonds       : angle       3.98740 /  2.86 (  831)
  link_NAG-ASN         : bond        0.00679 /  0.36 (    5)
  link_NAG-ASN         : angle       2.73329 /  1.65 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1114.76 seconds
wall clock time: 20 minutes 0.25 seconds (1200.25 seconds total)