Starting phenix.real_space_refine
on Tue Mar  3 11:55:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dha_27434/03_2026/8dha_27434.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dha_27434/03_2026/8dha_27434.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dha_27434/03_2026/8dha_27434.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dha_27434/03_2026/8dha_27434.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dha_27434/03_2026/8dha_27434.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dha_27434/03_2026/8dha_27434.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.014
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      16      5.16       5
     C    2234      2.51       5
     N     596      2.21       5
     O     664      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  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: 3510
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 773
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 773
          Classifications: {'peptide': 94}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 89}
    Chain: "B"
      Number of atoms: 1622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 204, 1622
          Classifications: {'peptide': 204}
          Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 188}
    Chain: "C"
      Number of atoms: 1087
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 141, 1087
          Classifications: {'peptide': 141}
          Link IDs: {'PTRANS': 6, 'TRANS': 134}
    Chain: "A"
      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
    Chain: "B"
      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: 0.92, per 1000 atoms: 0.26
  Number of scatterers: 3510
  At special positions: 0
  Unit cell: (103.786, 72.7693, 95.4352, 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      16     16.00
     O     664      8.00
     N     596      7.00
     C    2234      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 350 " - pdb=" SG  CYS A 410 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 411 " - pdb=" SG  CYS A 416 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 434 " - pdb=" SG  CYS B 445 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 471 " - pdb=" SG  CYS B 526 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 486 " - pdb=" SG  CYS B 496 " 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 901 " - " ASN A 345 "
      " NAG B 901 " - " ASN B 622 "
  Time building additional restraints: 0.21
  Conformation dependent library (CDL) restraints added in 135.2 milliseconds
  

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  844

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 9 sheets defined
      25.7% alpha, 26.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 375 through 377
      No H-bonds generated for 'chain 'A' and resid 375 through 377'
    Processing helix  chain 'B' and resid 528 through 533
      removed outlier: 3.739A  pdb=" N   VAL B 532 " --> pdb=" O   PRO B 529 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   VAL B 533 " --> pdb=" O   ASP B 530 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2 through 26
    Processing helix  chain 'C' and resid 50 through 67
    Processing helix  chain 'C' and resid 70 through 94
    Processing helix  chain 'C' and resid 107 through 117
      removed outlier: 3.554A  pdb=" N   ASP C 111 " --> pdb=" O   PRO C 107 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 117 through 141
      removed outlier: 4.393A  pdb=" N   ASP C 141 " --> pdb=" O   LEU C 137 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 337 through 339
      removed outlier: 5.963A  pdb=" N   ILE A 338 " --> pdb=" O   TYR A 424 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   VAL A 408 " --> pdb=" O   ALA A 421 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   VAL A 365 " --> pdb=" O   CYS A 411 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 337 through 339
      removed outlier: 5.963A  pdb=" N   ILE A 338 " --> pdb=" O   TYR A 424 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   VAL A 408 " --> pdb=" O   ALA A 421 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 346 through 347
      removed outlier: 3.788A  pdb=" N   ALA A 346 " --> pdb=" O   PHE A 391 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 353 through 354
    Processing sheet with id=AA5, first strand: chain 'B' and resid 432 through 436
      removed outlier: 3.516A  pdb=" N   MET B 443 " --> pdb=" O   PHE B 498 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   CYS B 445 " --> pdb=" O   CYS B 496 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   CYS B 496 " --> pdb=" O   CYS B 445 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   TRP B 447 " --> pdb=" O   TYR B 494 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   TYR B 494 " --> pdb=" O   TRP B 447 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 482 through 483
      removed outlier: 3.768A  pdb=" N   THR B 459 " --> pdb=" O   ASN B 514 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   ASN B 514 " --> pdb=" O   THR B 459 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   GLN B 461 " --> pdb=" O   ARG B 512 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ARG B 512 " --> pdb=" O   GLN B 461 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ARG B 463 " --> pdb=" O   TRP B 510 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LEU B 520 " --> pdb=" O   ILE B 513 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   HIS B 515 " --> pdb=" O   GLY B 518 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   GLY B 518 " --> pdb=" O   HIS B 515 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 482 through 483
      removed outlier: 3.768A  pdb=" N   THR B 459 " --> pdb=" O   ASN B 514 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   ASN B 514 " --> pdb=" O   THR B 459 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   GLN B 461 " --> pdb=" O   ARG B 512 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ARG B 512 " --> pdb=" O   GLN B 461 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ARG B 463 " --> pdb=" O   TRP B 510 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   TYR B 507 " --> pdb=" O   VAL B 527 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   VAL B 527 " --> pdb=" O   TYR B 507 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   MET B 509 " --> pdb=" O   THR B 525 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   THR B 525 " --> pdb=" O   MET B 509 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 542 through 545
      removed outlier: 3.816A  pdb=" N   LYS B 542 " --> pdb=" O   SER B 555 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   SER B 555 " --> pdb=" O   LYS B 542 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   VAL B 554 " --> pdb=" O   ALA B 594 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 582 through 586
      removed outlier: 3.933A  pdb=" N   VAL B 607 " --> pdb=" O   ALA B 627 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   ALA B 627 " --> pdb=" O   VAL B 607 " (cutoff:3.500A)

    137 hydrogen bonds defined for protein.
    375 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: 0.36

  Time building geometry restraints manager: 0.33 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1122
        1.34 -     1.46: 788
        1.46 -     1.58: 1658
        1.58 -     1.70: 1
        1.70 -     1.81: 19
  Bond restraints: 3588
  Sorted by residual:
  bond pdb=" CB  PRO B 472 "
       pdb=" CG  PRO B 472 "
    ideal  model  delta    sigma   weight residual
    1.492  1.614 -0.122 5.00e-02 4.00e+02 5.94e+00
  bond pdb=" C2  NAG A 901 "
       pdb=" N2  NAG A 901 "
    ideal  model  delta    sigma   weight residual
    1.439  1.463 -0.024 2.00e-02 2.50e+03 1.40e+00
  bond pdb=" C1  NAG B 901 "
       pdb=" O5  NAG B 901 "
    ideal  model  delta    sigma   weight residual
    1.406  1.430 -0.024 2.00e-02 2.50e+03 1.39e+00
  bond pdb=" C5  NAG A 901 "
       pdb=" O5  NAG A 901 "
    ideal  model  delta    sigma   weight residual
    1.413  1.434 -0.021 2.00e-02 2.50e+03 1.14e+00
  bond pdb=" C5  NAG B 901 "
       pdb=" O5  NAG B 901 "
    ideal  model  delta    sigma   weight residual
    1.413  1.434 -0.021 2.00e-02 2.50e+03 1.10e+00
  ... (remaining 3583 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.22: 4777
        2.22 -     4.44: 91
        4.44 -     6.67: 11
        6.67 -     8.89: 4
        8.89 -    11.11: 1
  Bond angle restraints: 4884
  Sorted by residual:
  angle pdb=" CA  SER B 450 "
        pdb=" C   SER B 450 "
        pdb=" N   THR B 451 "
      ideal   model   delta    sigma   weight residual
     116.84  125.69   -8.85 1.71e+00 3.42e-01 2.68e+01
  angle pdb=" CA  PRO B 472 "
        pdb=" N   PRO B 472 "
        pdb=" CD  PRO B 472 "
      ideal   model   delta    sigma   weight residual
     112.00  104.86    7.14 1.40e+00 5.10e-01 2.60e+01
  angle pdb=" CA  SER B 450 "
        pdb=" C   SER B 450 "
        pdb=" O   SER B 450 "
      ideal   model   delta    sigma   weight residual
     120.51  115.41    5.10 1.43e+00 4.89e-01 1.27e+01
  angle pdb=" N   LYS C   5 "
        pdb=" CA  LYS C   5 "
        pdb=" C   LYS C   5 "
      ideal   model   delta    sigma   weight residual
     111.28  107.66    3.62 1.09e+00 8.42e-01 1.10e+01
  angle pdb=" CA  LEU C 104 "
        pdb=" CB  LEU C 104 "
        pdb=" CG  LEU C 104 "
      ideal   model   delta    sigma   weight residual
     116.30  127.41  -11.11 3.50e+00 8.16e-02 1.01e+01
  ... (remaining 4879 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 1869
       17.93 -    35.86: 279
       35.86 -    53.79: 56
       53.79 -    71.72: 9
       71.72 -    89.64: 4
  Dihedral angle restraints: 2217
    sinusoidal: 919
      harmonic: 1298
  Sorted by residual:
  dihedral pdb=" CB  CYS B 486 "
           pdb=" SG  CYS B 486 "
           pdb=" SG  CYS B 496 "
           pdb=" CB  CYS B 496 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   55.09   37.91     1      1.00e+01 1.00e-02 2.03e+01
  dihedral pdb=" CB  GLU B 435 "
           pdb=" CG  GLU B 435 "
           pdb=" CD  GLU B 435 "
           pdb=" OE1 GLU B 435 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.64  -89.64     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CG  ARG C  35 "
           pdb=" CD  ARG C  35 "
           pdb=" NE  ARG C  35 "
           pdb=" CZ  ARG C  35 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -135.34  -44.66     2      1.50e+01 4.44e-03 1.05e+01
  ... (remaining 2214 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 381
       0.039 -    0.077: 135
       0.077 -    0.116: 47
       0.116 -    0.154: 7
       0.154 -    0.193: 2
  Chirality restraints: 572
  Sorted by residual:
  chirality pdb=" C1  NAG B 901 "
            pdb=" ND2 ASN B 622 "
            pdb=" C2  NAG B 901 "
            pdb=" O5  NAG B 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.21   -0.19 2.00e-01 2.50e+01 9.29e-01
  chirality pdb=" C2  NAG A 901 "
            pdb=" C1  NAG A 901 "
            pdb=" C3  NAG A 901 "
            pdb=" N2  NAG A 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.31   -0.18 2.00e-01 2.50e+01 7.89e-01
  chirality pdb=" CB  VAL C 113 "
            pdb=" CA  VAL C 113 "
            pdb=" CG1 VAL C 113 "
            pdb=" CG2 VAL C 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.49   -0.14 2.00e-01 2.50e+01 5.01e-01
  ... (remaining 569 not shown)

  Planarity restraints: 616
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS B 471 "    0.048 5.00e-02 4.00e+02   6.92e-02 7.67e+00
        pdb=" N   PRO B 472 "   -0.120 5.00e-02 4.00e+02
        pdb=" CA  PRO B 472 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 472 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 374 "    0.038 5.00e-02 4.00e+02   5.81e-02 5.39e+00
        pdb=" N   PRO A 375 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO A 375 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 375 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 447 "    0.012 2.00e-02 2.50e+03   1.21e-02 3.66e+00
        pdb=" CG  TRP B 447 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 447 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 447 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 447 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 447 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 447 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 447 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 447 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 447 "    0.002 2.00e-02 2.50e+03
  ... (remaining 613 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.70: 139
        2.70 -     3.25: 3307
        3.25 -     3.80: 5152
        3.80 -     4.35: 5698
        4.35 -     4.90: 9630
  Nonbonded interactions: 23926
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 563 "
            pdb=" OG1 THR C  19 "
     model   vdw
     2.155 3.040
  nonbonded pdb=" O   VAL C  64 "
            pdb=" OG  SER C  67 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" O   LEU B 455 "
            pdb=" OG  SER B 458 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" OH  TYR B 470 "
            pdb=" OD2 ASP C   9 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" O   ILE B 511 "
            pdb=" OG  SER B 522 "
     model   vdw
     2.304 3.040
  ... (remaining 23921 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:             1.160
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.870
  Find NCS groups from input model:        0.010
  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:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7290
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.122   3595  Z= 0.153
  Angle     :  0.775  11.108   4900  Z= 0.395
  Chirality :  0.045   0.193    572
  Planarity :  0.005   0.069    614
  Dihedral  : 17.096  89.644   1358
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 14.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 34.07 %
    Favored  : 65.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.08 (0.41), residues: 433
  helix:  2.17 (0.52), residues: 106
  sheet:  0.30 (0.54), residues: 103
  loop : -1.15 (0.41), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 571 
 TYR   0.014   0.001   TYR B 605 
 PHE   0.012   0.001   PHE B 502 
 TRP   0.033   0.003   TRP B 447 
 HIS   0.002   0.001   HIS A 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 3588)
  covalent geometry    : angle       0.76308 ( 4884)
  SS BOND              : bond        0.00185 (    5)
  SS BOND              : angle       0.73446 (   10)
  hydrogen bonds       : bond        0.21508 (  129)
  hydrogen bonds       : angle       7.64563 (  375)
  link_NAG-ASN         : bond        0.00305 (    2)
  link_NAG-ASN         : angle       3.99882 (    6)

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 87
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  403 PHE cc_start: 0.9397 (m-80) cc_final: 0.8920 (m-10)
REVERT: B  504 LEU cc_start: 0.9139 (mp) cc_final: 0.8809 (tt)
REVERT: C   87 LEU cc_start: 0.8920 (mt) cc_final: 0.8684 (mt)
  outliers start: 2
  outliers final: 1
  residues processed: 87
  average time/residue: 0.0638
  time to fit residues: 6.8805
Evaluate side-chains
  82 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 81
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  569 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 414 GLN
** B 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 608 GLN
C  28 GLN
** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.107366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.074045 restraints weight = 11007.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.075761 restraints weight = 5881.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.076710 restraints weight = 4422.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.077166 restraints weight = 3880.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 16)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.077167 restraints weight = 3653.034|
|-----------------------------------------------------------------------------|
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7291
moved from start:          0.1369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   3595  Z= 0.186
  Angle     :  0.727   9.396   4900  Z= 0.359
  Chirality :  0.046   0.230    572
  Planarity :  0.005   0.045    614
  Dihedral  :  6.474  50.331    518
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 10.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 28.15 %
    Favored  : 66.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.03 (0.41), residues: 433
  helix:  2.03 (0.51), residues: 110
  sheet:  0.36 (0.52), residues: 102
  loop : -1.34 (0.40), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 613 
 TYR   0.016   0.002   TYR B 605 
 PHE   0.011   0.002   PHE B 502 
 TRP   0.026   0.002   TRP B 447 
 HIS   0.002   0.001   HIS B 515 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 3588)
  covalent geometry    : angle       0.71343 ( 4884)
  SS BOND              : bond        0.00354 (    5)
  SS BOND              : angle       0.88107 (   10)
  hydrogen bonds       : bond        0.04509 (  129)
  hydrogen bonds       : angle       5.86047 (  375)
  link_NAG-ASN         : bond        0.00279 (    2)
  link_NAG-ASN         : angle       4.07171 (    6)

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 82
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  350 CYS cc_start: 0.5876 (OUTLIER) cc_final: 0.5428 (t)
REVERT: A  417 HIS cc_start: 0.5796 (OUTLIER) cc_final: 0.5454 (t-90)
REVERT: B  444 THR cc_start: 0.9228 (m) cc_final: 0.8989 (t)
REVERT: B  447 TRP cc_start: 0.8354 (p-90) cc_final: 0.7764 (p-90)
REVERT: B  504 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8661 (tt)
REVERT: B  554 VAL cc_start: 0.8723 (t) cc_final: 0.8473 (t)
REVERT: B  556 TRP cc_start: 0.8999 (p90) cc_final: 0.8512 (p90)
REVERT: B  569 GLN cc_start: 0.6938 (tt0) cc_final: 0.6683 (tt0)
REVERT: B  620 TRP cc_start: 0.7612 (m100) cc_final: 0.7248 (m100)
REVERT: B  623 TRP cc_start: 0.8083 (m100) cc_final: 0.6652 (m100)
  outliers start: 20
  outliers final: 11
  residues processed: 97
  average time/residue: 0.0553
  time to fit residues: 6.8267
Evaluate side-chains
  90 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  350 CYS
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  417 HIS
Chi-restraints excluded: chain B residue  451 THR
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  541 VAL
Chi-restraints excluded: chain B residue  598 VAL
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain C residue   88 HIS
Chi-restraints excluded: chain C residue  130 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0980
   chunk 34 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 41 optimal weight:    3.9990
   chunk 2 optimal weight:    0.4980
   chunk 19 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B 499 GLN
** B 564 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 = 0.3506 r_free = 0.3506 target = 0.108246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.074874 restraints weight = 10890.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.076663 restraints weight = 5802.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.077611 restraints weight = 4371.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.078107 restraints weight = 3832.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.078317 restraints weight = 3596.154|
|-----------------------------------------------------------------------------|
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7261
moved from start:          0.1701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3595  Z= 0.145
  Angle     :  0.706  11.785   4900  Z= 0.338
  Chirality :  0.046   0.236    572
  Planarity :  0.004   0.048    614
  Dihedral  :  5.951  52.418    515
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 28.15 %
    Favored  : 66.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.40), residues: 433
  helix:  2.00 (0.51), residues: 110
  sheet:  0.31 (0.53), residues: 93
  loop : -1.32 (0.39), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 613 
 TYR   0.014   0.001   TYR B 605 
 PHE   0.027   0.002   PHE C  41 
 TRP   0.021   0.002   TRP A 366 
 HIS   0.002   0.001   HIS B 465 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 3588)
  covalent geometry    : angle       0.66953 ( 4884)
  SS BOND              : bond        0.00280 (    5)
  SS BOND              : angle       0.60401 (   10)
  hydrogen bonds       : bond        0.04225 (  129)
  hydrogen bonds       : angle       5.46427 (  375)
  link_NAG-ASN         : bond        0.01104 (    2)
  link_NAG-ASN         : angle       6.43169 (    6)

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 78
  time to evaluate  : 0.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  350 CYS cc_start: 0.5850 (OUTLIER) cc_final: 0.5348 (t)
REVERT: A  417 HIS cc_start: 0.5858 (OUTLIER) cc_final: 0.5580 (t-90)
REVERT: B  447 TRP cc_start: 0.8386 (p-90) cc_final: 0.7479 (p-90)
REVERT: B  504 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8471 (tt)
REVERT: B  509 MET cc_start: 0.8327 (ppp) cc_final: 0.7305 (ppp)
REVERT: B  556 TRP cc_start: 0.8923 (p90) cc_final: 0.8559 (p90)
REVERT: B  620 TRP cc_start: 0.7680 (m100) cc_final: 0.7372 (m100)
  outliers start: 23
  outliers final: 14
  residues processed: 96
  average time/residue: 0.0516
  time to fit residues: 6.2457
Evaluate side-chains
  90 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 73
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  350 CYS
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  417 HIS
Chi-restraints excluded: chain B residue  451 THR
Chi-restraints excluded: chain B residue  487 VAL
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  544 GLU
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  598 VAL
Chi-restraints excluded: chain C residue   19 THR
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain C residue   88 HIS
Chi-restraints excluded: chain C residue  130 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 22 optimal weight:    0.3980
   chunk 38 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 1 optimal weight:    0.4980
   chunk 27 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   chunk 6 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 349 HIS
A 378 GLN
** B 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  75 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.108367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.075002 restraints weight = 10609.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.076765 restraints weight = 5655.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.077758 restraints weight = 4253.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.078203 restraints weight = 3714.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.078511 restraints weight = 3490.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7254
moved from start:          0.1879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3595  Z= 0.151
  Angle     :  0.692  10.894   4900  Z= 0.334
  Chirality :  0.046   0.238    572
  Planarity :  0.004   0.048    614
  Dihedral  :  5.784  51.753    515
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  7.16 %
    Allowed  : 26.42 %
    Favored  : 66.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.20 (0.40), residues: 433
  helix:  1.97 (0.51), residues: 110
  sheet:  0.13 (0.52), residues: 98
  loop : -1.39 (0.40), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 613 
 TYR   0.012   0.001   TYR B 605 
 PHE   0.019   0.002   PHE C  41 
 TRP   0.023   0.002   TRP A 366 
 HIS   0.002   0.001   HIS B 465 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 3588)
  covalent geometry    : angle       0.66090 ( 4884)
  SS BOND              : bond        0.00256 (    5)
  SS BOND              : angle       0.88363 (   10)
  hydrogen bonds       : bond        0.04104 (  129)
  hydrogen bonds       : angle       5.37712 (  375)
  link_NAG-ASN         : bond        0.00476 (    2)
  link_NAG-ASN         : angle       5.82283 (    6)

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 77
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  350 CYS cc_start: 0.5919 (OUTLIER) cc_final: 0.5360 (t)
REVERT: A  417 HIS cc_start: 0.5902 (OUTLIER) cc_final: 0.5586 (t-90)
REVERT: B  447 TRP cc_start: 0.8409 (p-90) cc_final: 0.7494 (p-90)
REVERT: B  504 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8496 (tt)
REVERT: B  509 MET cc_start: 0.8274 (ppp) cc_final: 0.7210 (ppp)
REVERT: B  530 ASP cc_start: 0.8562 (t70) cc_final: 0.8277 (t70)
REVERT: B  556 TRP cc_start: 0.9088 (p90) cc_final: 0.8631 (p90)
  outliers start: 29
  outliers final: 17
  residues processed: 101
  average time/residue: 0.0526
  time to fit residues: 6.8732
Evaluate side-chains
  93 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 73
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  350 CYS
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  410 CYS
Chi-restraints excluded: chain A residue  417 HIS
Chi-restraints excluded: chain B residue  487 VAL
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  541 VAL
Chi-restraints excluded: chain B residue  544 GLU
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  598 VAL
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain C residue   75 GLN
Chi-restraints excluded: chain C residue   88 HIS
Chi-restraints excluded: chain C residue  126 LEU
Chi-restraints excluded: chain C residue  130 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 31 optimal weight:    6.9990
   chunk 3 optimal weight:    1.9990
   chunk 39 optimal weight:    0.1980
   chunk 35 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 36 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** B 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.108621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.075446 restraints weight = 10917.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.077215 restraints weight = 5802.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.078148 restraints weight = 4347.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.078673 restraints weight = 3810.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.078912 restraints weight = 3564.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7222
moved from start:          0.2061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3595  Z= 0.147
  Angle     :  0.702   9.993   4900  Z= 0.335
  Chirality :  0.046   0.239    572
  Planarity :  0.004   0.045    614
  Dihedral  :  5.682  51.928    515
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 28.89 %
    Favored  : 65.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.40), residues: 433
  helix:  1.89 (0.51), residues: 110
  sheet:  0.14 (0.53), residues: 98
  loop : -1.36 (0.40), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 610 
 TYR   0.012   0.001   TYR A 409 
 PHE   0.015   0.002   PHE C  41 
 TRP   0.012   0.002   TRP A 366 
 HIS   0.006   0.001   HIS A 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 3588)
  covalent geometry    : angle       0.67686 ( 4884)
  SS BOND              : bond        0.00236 (    5)
  SS BOND              : angle       0.69795 (   10)
  hydrogen bonds       : bond        0.04028 (  129)
  hydrogen bonds       : angle       5.29906 (  375)
  link_NAG-ASN         : bond        0.00396 (    2)
  link_NAG-ASN         : angle       5.40979 (    6)

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 79
  time to evaluate  : 0.099 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  350 CYS cc_start: 0.6015 (OUTLIER) cc_final: 0.5374 (t)
REVERT: A  409 TYR cc_start: 0.5830 (m-80) cc_final: 0.5620 (m-80)
REVERT: B  447 TRP cc_start: 0.8363 (p-90) cc_final: 0.7275 (p-90)
REVERT: B  504 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8559 (tt)
REVERT: B  530 ASP cc_start: 0.8563 (t70) cc_final: 0.8214 (t70)
REVERT: B  556 TRP cc_start: 0.9088 (p90) cc_final: 0.8547 (p90)
REVERT: B  623 TRP cc_start: 0.8138 (m100) cc_final: 0.7245 (m100)
  outliers start: 21
  outliers final: 16
  residues processed: 96
  average time/residue: 0.0528
  time to fit residues: 6.5595
Evaluate side-chains
  94 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 76
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  350 CYS
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  410 CYS
Chi-restraints excluded: chain B residue  487 VAL
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  541 VAL
Chi-restraints excluded: chain B residue  544 GLU
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  598 VAL
Chi-restraints excluded: chain C residue    1 VAL
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain C residue   88 HIS
Chi-restraints excluded: chain C residue  130 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 39 optimal weight:    0.0060
   chunk 0 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9980
   chunk 40 optimal weight:    0.6980
   chunk 13 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.6596

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

Flipped N/Q/H residues before XYZ refinement:
** B 564 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 = 0.3501 r_free = 0.3501 target = 0.108040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.074733 restraints weight = 10883.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.076482 restraints weight = 5813.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.077469 restraints weight = 4365.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.077979 restraints weight = 3810.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.078221 restraints weight = 3571.616|
|-----------------------------------------------------------------------------|
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7252
moved from start:          0.2212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3595  Z= 0.145
  Angle     :  0.700   9.380   4900  Z= 0.333
  Chirality :  0.045   0.238    572
  Planarity :  0.004   0.043    614
  Dihedral  :  5.618  51.855    515
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 11.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 28.15 %
    Favored  : 66.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.15 (0.41), residues: 433
  helix:  1.94 (0.51), residues: 110
  sheet:  0.12 (0.51), residues: 102
  loop : -1.31 (0.41), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 610 
 TYR   0.011   0.002   TYR A 409 
 PHE   0.013   0.002   PHE C  41 
 TRP   0.011   0.002   TRP B 620 
 HIS   0.005   0.001   HIS A 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 3588)
  covalent geometry    : angle       0.67853 ( 4884)
  SS BOND              : bond        0.00213 (    5)
  SS BOND              : angle       0.64145 (   10)
  hydrogen bonds       : bond        0.03953 (  129)
  hydrogen bonds       : angle       5.24682 (  375)
  link_NAG-ASN         : bond        0.00388 (    2)
  link_NAG-ASN         : angle       4.96216 (    6)

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 79
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  504 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8543 (tt)
REVERT: B  530 ASP cc_start: 0.8696 (t70) cc_final: 0.8452 (t70)
REVERT: B  556 TRP cc_start: 0.9090 (p90) cc_final: 0.8479 (p90)
REVERT: B  623 TRP cc_start: 0.8111 (m100) cc_final: 0.7209 (m100)
  outliers start: 23
  outliers final: 19
  residues processed: 97
  average time/residue: 0.0527
  time to fit residues: 6.6188
Evaluate side-chains
  95 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 75
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  410 CYS
Chi-restraints excluded: chain B residue  478 HIS
Chi-restraints excluded: chain B residue  487 VAL
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  541 VAL
Chi-restraints excluded: chain B residue  544 GLU
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  598 VAL
Chi-restraints excluded: chain C residue    1 VAL
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain C residue   88 HIS
Chi-restraints excluded: chain C residue  130 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 14 optimal weight:    0.3980
   chunk 36 optimal weight:    0.2980
   chunk 13 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 39 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 15 optimal weight:    0.4980
   chunk 37 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
B 608 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.108696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.075287 restraints weight = 11009.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.077087 restraints weight = 5870.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.078085 restraints weight = 4379.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.078578 restraints weight = 3813.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.078578 restraints weight = 3575.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7292
moved from start:          0.2327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3595  Z= 0.134
  Angle     :  0.692   9.424   4900  Z= 0.328
  Chirality :  0.045   0.239    572
  Planarity :  0.004   0.042    614
  Dihedral  :  5.580  52.308    515
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 10.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 29.14 %
    Favored  : 65.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.13 (0.41), residues: 433
  helix:  1.90 (0.51), residues: 110
  sheet:  0.39 (0.52), residues: 97
  loop : -1.38 (0.41), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 368 
 TYR   0.034   0.002   TYR A 409 
 PHE   0.011   0.002   PHE C  41 
 TRP   0.014   0.002   TRP B 447 
 HIS   0.005   0.001   HIS A 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 3588)
  covalent geometry    : angle       0.67325 ( 4884)
  SS BOND              : bond        0.00224 (    5)
  SS BOND              : angle       0.58402 (   10)
  hydrogen bonds       : bond        0.03875 (  129)
  hydrogen bonds       : angle       5.16618 (  375)
  link_NAG-ASN         : bond        0.00323 (    2)
  link_NAG-ASN         : angle       4.70228 (    6)

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 76
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  350 CYS cc_start: 0.5679 (OUTLIER) cc_final: 0.5166 (t)
REVERT: B  447 TRP cc_start: 0.8547 (p-90) cc_final: 0.7444 (p-90)
REVERT: B  530 ASP cc_start: 0.8581 (t70) cc_final: 0.8342 (t70)
REVERT: B  556 TRP cc_start: 0.9076 (p90) cc_final: 0.8433 (p90)
REVERT: C    9 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.8108 (t0)
  outliers start: 21
  outliers final: 17
  residues processed: 93
  average time/residue: 0.0560
  time to fit residues: 6.6576
Evaluate side-chains
  92 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 73
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  350 CYS
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  410 CYS
Chi-restraints excluded: chain B residue  478 HIS
Chi-restraints excluded: chain B residue  487 VAL
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  541 VAL
Chi-restraints excluded: chain B residue  544 GLU
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  598 VAL
Chi-restraints excluded: chain C residue    9 ASP
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain C residue   88 HIS
Chi-restraints excluded: chain C residue  130 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0470
   chunk 16 optimal weight:    0.4980
   chunk 36 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 39 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0000
   chunk 6 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.4482

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.110727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.077575 restraints weight = 11173.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.079364 restraints weight = 6015.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.080375 restraints weight = 4508.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.080888 restraints weight = 3922.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.080888 restraints weight = 3671.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7240
moved from start:          0.2469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3595  Z= 0.122
  Angle     :  0.689   9.540   4900  Z= 0.323
  Chirality :  0.045   0.238    572
  Planarity :  0.004   0.043    614
  Dihedral  :  5.502  52.836    515
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 30.12 %
    Favored  : 65.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.41), residues: 433
  helix:  1.93 (0.51), residues: 110
  sheet:  0.44 (0.51), residues: 97
  loop : -1.39 (0.40), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 368 
 TYR   0.027   0.002   TYR A 409 
 PHE   0.011   0.001   PHE C  41 
 TRP   0.012   0.001   TRP B 447 
 HIS   0.004   0.001   HIS A 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 3588)
  covalent geometry    : angle       0.67157 ( 4884)
  SS BOND              : bond        0.00217 (    5)
  SS BOND              : angle       0.54397 (   10)
  hydrogen bonds       : bond        0.03774 (  129)
  hydrogen bonds       : angle       5.05232 (  375)
  link_NAG-ASN         : bond        0.00279 (    2)
  link_NAG-ASN         : angle       4.44896 (    6)

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 77
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  350 CYS cc_start: 0.5584 (OUTLIER) cc_final: 0.5249 (t)
REVERT: A  366 TRP cc_start: 0.8493 (m100) cc_final: 0.8248 (m100)
REVERT: B  530 ASP cc_start: 0.8572 (t70) cc_final: 0.8315 (t70)
REVERT: B  556 TRP cc_start: 0.9043 (p90) cc_final: 0.8381 (p90)
REVERT: B  563 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8319 (mt-10)
REVERT: C    9 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7983 (t0)
  outliers start: 18
  outliers final: 15
  residues processed: 93
  average time/residue: 0.0523
  time to fit residues: 6.1869
Evaluate side-chains
  93 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 76
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 CYS
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  387 SER
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  410 CYS
Chi-restraints excluded: chain B residue  478 HIS
Chi-restraints excluded: chain B residue  487 VAL
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  541 VAL
Chi-restraints excluded: chain B residue  544 GLU
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain C residue    9 ASP
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain C residue   88 HIS
Chi-restraints excluded: chain C residue  130 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0050
   chunk 1 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 32 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 21 optimal weight:    0.2980
   chunk 31 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0980
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.3394

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.111992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.078606 restraints weight = 10716.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.080394 restraints weight = 5821.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.081386 restraints weight = 4371.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.081890 restraints weight = 3813.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.082086 restraints weight = 3576.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7211
moved from start:          0.2599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3595  Z= 0.109
  Angle     :  0.669   9.443   4900  Z= 0.314
  Chirality :  0.044   0.237    572
  Planarity :  0.004   0.042    614
  Dihedral  :  5.397  53.713    515
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 29.63 %
    Favored  : 65.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.12 (0.41), residues: 433
  helix:  1.86 (0.51), residues: 110
  sheet:  0.49 (0.53), residues: 93
  loop : -1.36 (0.40), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 610 
 TYR   0.024   0.001   TYR A 409 
 PHE   0.010   0.001   PHE C  41 
 TRP   0.016   0.002   TRP B 447 
 HIS   0.003   0.001   HIS A 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 3588)
  covalent geometry    : angle       0.65358 ( 4884)
  SS BOND              : bond        0.00201 (    5)
  SS BOND              : angle       0.54068 (   10)
  hydrogen bonds       : bond        0.03548 (  129)
  hydrogen bonds       : angle       4.95203 (  375)
  link_NAG-ASN         : bond        0.00303 (    2)
  link_NAG-ASN         : angle       4.19161 (    6)

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  350 CYS cc_start: 0.5445 (OUTLIER) cc_final: 0.5163 (t)
REVERT: A  366 TRP cc_start: 0.8499 (m100) cc_final: 0.8220 (m100)
REVERT: A  402 LYS cc_start: 0.9372 (pptt) cc_final: 0.9160 (pptt)
REVERT: B  447 TRP cc_start: 0.8484 (p-90) cc_final: 0.7328 (p-90)
REVERT: B  556 TRP cc_start: 0.9010 (p90) cc_final: 0.8376 (p90)
REVERT: B  563 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8476 (mt-10)
REVERT: B  623 TRP cc_start: 0.8075 (m100) cc_final: 0.7274 (m100)
REVERT: C    5 LYS cc_start: 0.7638 (tptt) cc_final: 0.7438 (tptt)
REVERT: C    9 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7709 (t0)
  outliers start: 19
  outliers final: 15
  residues processed: 93
  average time/residue: 0.0489
  time to fit residues: 5.8875
Evaluate side-chains
  93 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 76
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 CYS
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  387 SER
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  410 CYS
Chi-restraints excluded: chain B residue  478 HIS
Chi-restraints excluded: chain B residue  487 VAL
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  541 VAL
Chi-restraints excluded: chain B residue  544 GLU
Chi-restraints excluded: chain C residue    9 ASP
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain C residue   88 HIS
Chi-restraints excluded: chain C residue  130 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 18 optimal weight:    0.5980
   chunk 38 optimal weight:    0.0980
   chunk 26 optimal weight:    0.0970
   chunk 29 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 31 optimal weight:    6.9990
   chunk 0 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.4778

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.110347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.076661 restraints weight = 10996.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.078489 restraints weight = 5829.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.079473 restraints weight = 4336.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.080008 restraints weight = 3775.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.080194 restraints weight = 3529.799|
|-----------------------------------------------------------------------------|
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7274
moved from start:          0.2623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3595  Z= 0.123
  Angle     :  0.700  10.144   4900  Z= 0.325
  Chirality :  0.045   0.240    572
  Planarity :  0.004   0.043    614
  Dihedral  :  5.346  52.028    515
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 30.12 %
    Favored  : 65.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.16 (0.40), residues: 433
  helix:  1.88 (0.51), residues: 110
  sheet:  0.42 (0.53), residues: 90
  loop : -1.37 (0.39), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 368 
 TYR   0.022   0.001   TYR A 409 
 PHE   0.010   0.001   PHE C  41 
 TRP   0.013   0.002   TRP B 447 
 HIS   0.004   0.001   HIS A 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 3588)
  covalent geometry    : angle       0.68619 ( 4884)
  SS BOND              : bond        0.00186 (    5)
  SS BOND              : angle       0.59729 (   10)
  hydrogen bonds       : bond        0.03614 (  129)
  hydrogen bonds       : angle       4.99691 (  375)
  link_NAG-ASN         : bond        0.00282 (    2)
  link_NAG-ASN         : angle       4.10634 (    6)

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 75
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  350 CYS cc_start: 0.5447 (OUTLIER) cc_final: 0.5188 (t)
REVERT: A  366 TRP cc_start: 0.8536 (m100) cc_final: 0.8275 (m100)
REVERT: A  402 LYS cc_start: 0.9374 (pptt) cc_final: 0.9158 (pptt)
REVERT: B  556 TRP cc_start: 0.9049 (p90) cc_final: 0.8415 (p90)
REVERT: C    9 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.7855 (t0)
  outliers start: 16
  outliers final: 14
  residues processed: 88
  average time/residue: 0.0571
  time to fit residues: 6.4163
Evaluate side-chains
  90 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 74
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 CYS
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  410 CYS
Chi-restraints excluded: chain B residue  478 HIS
Chi-restraints excluded: chain B residue  487 VAL
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  541 VAL
Chi-restraints excluded: chain B residue  544 GLU
Chi-restraints excluded: chain C residue    9 ASP
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain C residue   88 HIS
Chi-restraints excluded: chain C residue  130 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 24 optimal weight:    0.3980
   chunk 22 optimal weight:    4.9990
   chunk 23 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 37 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** B 564 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 = 0.3517 r_free = 0.3517 target = 0.109141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.075439 restraints weight = 10535.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.077207 restraints weight = 5607.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.078207 restraints weight = 4199.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.078690 restraints weight = 3659.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.078850 restraints weight = 3435.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
moved from start:          0.2645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3595  Z= 0.143
  Angle     :  0.709  10.359   4900  Z= 0.334
  Chirality :  0.045   0.238    572
  Planarity :  0.004   0.044    614
  Dihedral  :  5.418  51.271    515
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 29.14 %
    Favored  : 66.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.22 (0.40), residues: 433
  helix:  1.69 (0.50), residues: 110
  sheet:  0.38 (0.53), residues: 92
  loop : -1.33 (0.40), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 610 
 TYR   0.022   0.002   TYR A 409 
 PHE   0.010   0.001   PHE C  41 
 TRP   0.016   0.002   TRP B 447 
 HIS   0.004   0.001   HIS A 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 3588)
  covalent geometry    : angle       0.69470 ( 4884)
  SS BOND              : bond        0.00212 (    5)
  SS BOND              : angle       0.67997 (   10)
  hydrogen bonds       : bond        0.03818 (  129)
  hydrogen bonds       : angle       5.08853 (  375)
  link_NAG-ASN         : bond        0.00271 (    2)
  link_NAG-ASN         : angle       4.04274 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 877.44 seconds
wall clock time: 15 minutes 41.23 seconds (941.23 seconds total)