Starting phenix.real_space_refine
on Fri Aug 22 16:41:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pg0_17655/08_2025/8pg0_17655.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pg0_17655/08_2025/8pg0_17655.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.97
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pg0_17655/08_2025/8pg0_17655.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pg0_17655/08_2025/8pg0_17655.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pg0_17655/08_2025/8pg0_17655.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pg0_17655/08_2025/8pg0_17655.map"
  }
  resolution = 2.97
  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=   0.001
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      38      5.16       5
     C    3826      2.51       5
     N     912      2.21       5
     O    1040      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5816
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3986
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 511, 3978
          Classifications: {'peptide': 511}
          Link IDs: {'PTRANS': 17, 'TRANS': 493}
          Chain breaks: 8
      Conformer: "B"
        Number of residues, atoms: 511, 3978
          Classifications: {'peptide': 511}
          Link IDs: {'PTRANS': 17, 'TRANS': 493}
          Chain breaks: 8
          bond proxies already assigned to first conformer: 4066
    Chain: "H"
      Number of atoms: 970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 970
          Classifications: {'peptide': 125}
          Link IDs: {'PTRANS': 1, 'TRANS': 123}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 758
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 758
          Classifications: {'peptide': 101}
          Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 94}
    Chain: "A"
      Number of atoms: 102
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 102
          Unusual residues: {'BCT': 1, 'CLR': 3, 'NAG': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AASP A  70 " occ=0.58
      ... (14 atoms not shown)
      pdb=" OD2BASP A  70 " occ=0.42
  Time building chain proxies: 2.18, per 1000 atoms: 0.37
  Number of scatterers: 5816
  At special positions: 0
  Unit cell: (78.03, 119.85, 104.04, 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      38     16.00
     O    1040      8.00
     N     912      7.00
     C    3826      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 430 " - pdb=" SG  CYS A 530 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 459 " - pdb=" SG  CYS A 506 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 465 " - pdb=" SG  CYS A 485 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 474 " - pdb=" SG  CYS A 524 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 489 " - pdb=" SG  CYS A 504 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 599 " - pdb=" SG  CYS A 613 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " distance=2.04

  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 801 " - " ASN A 503 "
  Time building additional restraints: 0.46
  Conformation dependent library (CDL) restraints added in 435.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1338

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 8 sheets defined
      53.1% alpha, 12.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 51
    Processing helix  chain 'A' and resid 51 through 60
    Processing helix  chain 'A' and resid 62 through 85
      removed outlier: 4.048A  pdb=" N   PHE A  73 " --> pdb=" O   ILE A  69 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   GLU A  74 " --> pdb=" O  AASP A  70 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   VAL A  80 " --> pdb=" O   GLY A  76 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   VAL A  82 " --> pdb=" O   LEU A  78 " (cutoff:3.500A)
      removed outlier: 5.471A  pdb=" N   PHE A  83 " --> pdb=" O   LEU A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 113
    Processing helix  chain 'A' and resid 113 through 118
    Processing helix  chain 'A' and resid 170 through 186
      removed outlier: 4.033A  pdb=" N   VAL A 174 " --> pdb=" O   MET A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 200
    Processing helix  chain 'A' and resid 208 through 217
    Processing helix  chain 'A' and resid 217 through 231
      removed outlier: 3.966A  pdb=" N   VAL A 221 " --> pdb=" O   MET A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 274
      removed outlier: 3.696A  pdb=" N   GLY A 261 " --> pdb=" O   ALA A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 277
      No H-bonds generated for 'chain 'A' and resid 275 through 277'
    Processing helix  chain 'A' and resid 325 through 335
    Processing helix  chain 'A' and resid 335 through 358
      removed outlier: 3.928A  pdb=" N   TYR A 358 " --> pdb=" O   GLY A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 368
    Processing helix  chain 'A' and resid 370 through 401
      Proline residue:  A 384  - end of helix
      removed outlier: 3.946A  pdb=" N   PHE A 391 " --> pdb=" O   ALA A 387 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   GLY A 394 " --> pdb=" O   MET A 390 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ILE A 397 " --> pdb=" O   GLY A 393 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   LYS A 398 " --> pdb=" O   GLY A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 425
    Processing helix  chain 'A' and resid 457 through 462
      removed outlier: 3.834A  pdb=" N   GLU A 462 " --> pdb=" O   TYR A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 488
    Processing helix  chain 'A' and resid 504 through 508
      removed outlier: 3.888A  pdb=" N   GLU A 508 " --> pdb=" O   SER A 505 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 561
      removed outlier: 3.940A  pdb=" N   THR A 554 " --> pdb=" O   THR A 550 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   PHE A 555 " --> pdb=" O   GLY A 551 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   ILE A 556 " --> pdb=" O   GLY A 552 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   LEU A 557 " --> pdb=" O   THR A 553 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   VAL A 560 " --> pdb=" O   ILE A 556 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   LYS A 561 " --> pdb=" O   LEU A 557 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 566
      No H-bonds generated for 'chain 'A' and resid 564 through 566'
    Processing helix  chain 'A' and resid 567 through 585
    Processing helix  chain 'A' and resid 586 through 598
      removed outlier: 3.613A  pdb=" N   LEU A 594 " --> pdb=" O   TYR A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 617 through 649
      removed outlier: 4.060A  pdb=" N   SER A 629 " --> pdb=" O   TYR A 625 " (cutoff:3.500A)
      Proline residue:  A 635  - end of helix
      removed outlier: 4.008A  pdb=" N   LYS A 649 " --> pdb=" O   PHE A 645 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 3.911A  pdb=" N   PHE L  84 " --> pdb=" O   PRO L  81 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 436
      removed outlier: 3.527A  pdb=" N   CYS A 474 " --> pdb=" O   HIS A 520 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 491 through 492
      removed outlier: 3.641A  pdb=" N   SER A 491 " --> pdb=" O   TYR A 502 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 599 through 602
      removed outlier: 7.000A  pdb=" N   CYS A 599 " --> pdb=" O   TYR A 616 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   TYR A 616 " --> pdb=" O   CYS A 599 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   LYS A 601 " --> pdb=" O   ARG A 614 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 6 through 10
    Processing sheet with id=AA5, first strand: chain 'H' and resid 61 through 63
      removed outlier: 6.597A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   SER H  53 " --> pdb=" O   ILE H  37 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   ILE H  37 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 103 through 105
      removed outlier: 4.202A  pdb=" N   TYR H 103 " --> pdb=" O   ASP H 114 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 7
      removed outlier: 6.793A  pdb=" N   GLN L   4 " --> pdb=" O   SER L  27 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   THR L   6 " --> pdb=" O   ARG L  25 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 46 through 47

    327 hydrogen bonds defined for protein.
    946 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: 0.82

  Time building geometry restraints manager: 0.63 seconds

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

  Histogram of bond lengths:
        1.21 -     1.56: 5900
        1.56 -     1.91: 59
        1.91 -     2.25: 0
        2.25 -     2.60: 0
        2.60 -     2.95: 1
  Bond restraints: 5960
  Sorted by residual:
  bond pdb=" C   TYR L  50 "
       pdb=" N   SER L  53 "
    ideal  model  delta    sigma   weight residual
    1.329  2.947 -1.618 1.40e-02 5.10e+03 1.34e+04
  bond pdb=" C   ARG A 526 "
       pdb=" N   ASP A 527 "
    ideal  model  delta    sigma   weight residual
    1.328  1.432 -0.104 1.44e-02 4.82e+03 5.20e+01
  bond pdb=" C   VAL A 221 "
       pdb=" N   ILE A 222 "
    ideal  model  delta    sigma   weight residual
    1.335  1.282  0.053 1.26e-02 6.30e+03 1.77e+01
  bond pdb=" N   VAL A 563 "
       pdb=" CA  VAL A 563 "
    ideal  model  delta    sigma   weight residual
    1.456  1.494 -0.037 1.14e-02 7.69e+03 1.08e+01
  bond pdb=" N   GLY A 475 "
       pdb=" CA  GLY A 475 "
    ideal  model  delta    sigma   weight residual
    1.444  1.476 -0.031 1.06e-02 8.90e+03 8.83e+00
  ... (remaining 5955 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.46: 8074
        7.46 -    14.92: 3
       14.92 -    22.38: 0
       22.38 -    29.84: 0
       29.84 -    37.30: 1
  Bond angle restraints: 8078
  Sorted by residual:
  angle pdb=" C   TYR L  50 "
        pdb=" N   SER L  53 "
        pdb=" CA  SER L  53 "
      ideal   model   delta    sigma   weight residual
     121.70  159.00  -37.30 1.80e+00 3.09e-01 4.30e+02
  angle pdb=" N   ILE A 562 "
        pdb=" CA  ILE A 562 "
        pdb=" C   ILE A 562 "
      ideal   model   delta    sigma   weight residual
     112.29  107.96    4.33 9.40e-01 1.13e+00 2.12e+01
  angle pdb=" C   SER L  10 "
        pdb=" CA  SER L  10 "
        pdb=" CB  SER L  10 "
      ideal   model   delta    sigma   weight residual
     117.23  111.69    5.54 1.36e+00 5.41e-01 1.66e+01
  angle pdb=" N   ASN A 477 "
        pdb=" CA  ASN A 477 "
        pdb=" C   ASN A 477 "
      ideal   model   delta    sigma   weight residual
     113.19  108.58    4.61 1.19e+00 7.06e-01 1.50e+01
  angle pdb=" N   ASN A 476 "
        pdb=" CA  ASN A 476 "
        pdb=" C   ASN A 476 "
      ideal   model   delta    sigma   weight residual
     112.87  108.30    4.57 1.20e+00 6.94e-01 1.45e+01
  ... (remaining 8073 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.23: 3323
       24.23 -    48.45: 246
       48.45 -    72.68: 36
       72.68 -    96.90: 5
       96.90 -   121.13: 3
  Dihedral angle restraints: 3613
    sinusoidal: 1511
      harmonic: 2102
  Sorted by residual:
  dihedral pdb=" CA  TYR L  50 "
           pdb=" C   TYR L  50 "
           pdb=" N   SER L  53 "
           pdb=" CA  SER L  53 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00  -38.47   38.47     0      5.00e+00 4.00e-02 5.92e+01
  dihedral pdb=" CB  CYS A 459 "
           pdb=" SG  CYS A 459 "
           pdb=" SG  CYS A 506 "
           pdb=" CB  CYS A 506 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  131.42  -38.42     1      1.00e+01 1.00e-02 2.08e+01
  dihedral pdb=" CB  CYS A 474 "
           pdb=" SG  CYS A 474 "
           pdb=" SG  CYS A 524 "
           pdb=" CB  CYS A 524 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   55.20   37.80     1      1.00e+01 1.00e-02 2.01e+01
  ... (remaining 3610 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.083: 795
       0.083 -    0.166: 109
       0.166 -    0.250: 19
       0.250 -    0.333: 1
       0.333 -    0.416: 1
  Chirality restraints: 925
  Sorted by residual:
  chirality pdb=" C1  NAG A 801 "
            pdb=" ND2 ASN A 503 "
            pdb=" C2  NAG A 801 "
            pdb=" O5  NAG A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.98   -0.42 2.00e-01 2.50e+01 4.33e+00
  chirality pdb=" C13 CLR A 805 "
            pdb=" C12 CLR A 805 "
            pdb=" C14 CLR A 805 "
            pdb=" C17 CLR A 805 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.65   -0.28 2.00e-01 2.50e+01 2.00e+00
  chirality pdb=" C14 CLR A 805 "
            pdb=" C13 CLR A 805 "
            pdb=" C15 CLR A 805 "
            pdb=" C8  CLR A 805 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.56    0.24 2.00e-01 2.50e+01 1.43e+00
  ... (remaining 922 not shown)

  Planarity restraints: 970
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 801 "    0.270 2.00e-02 2.50e+03   2.28e-01 6.47e+02
        pdb=" C7  NAG A 801 "   -0.069 2.00e-02 2.50e+03
        pdb=" C8  NAG A 801 "    0.177 2.00e-02 2.50e+03
        pdb=" N2  NAG A 801 "   -0.387 2.00e-02 2.50e+03
        pdb=" O7  NAG A 801 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR L  50 "    0.023 2.00e-02 2.50e+03   4.05e-02 1.64e+01
        pdb=" C   TYR L  50 "   -0.069 2.00e-02 2.50e+03
        pdb=" O   TYR L  50 "    0.032 2.00e-02 2.50e+03
        pdb=" N   SER L  53 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 471 "    0.053 5.00e-02 4.00e+02   8.16e-02 1.07e+01
        pdb=" N   PRO A 472 "   -0.141 5.00e-02 4.00e+02
        pdb=" CA  PRO A 472 "    0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO A 472 "    0.043 5.00e-02 4.00e+02
  ... (remaining 967 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 586
        2.75 -     3.29: 6007
        3.29 -     3.82: 9912
        3.82 -     4.36: 12040
        4.36 -     4.90: 20237
  Nonbonded interactions: 48782
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN A 366 "
            pdb=" OG  SER A 618 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" O   PRO A 472 "
            pdb=" O   LEU A 521 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O   SER H  33 "
            pdb=" OG  SER H  57 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" O   SER A 228 "
            pdb=" OG  SER A 372 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" ND1 HIS A 115 "
            pdb=" O2  BCT A 802 "
     model   vdw
     2.299 3.120
  ... (remaining 48777 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=0.42 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             8.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.630
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.010
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
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      :  0.022   1.618   5969  Z= 1.552
  Angle     :  0.948  37.304   8097  Z= 0.587
  Chirality :  0.058   0.416    925
  Planarity :  0.009   0.228    969
  Dihedral  : 16.430 121.126   2251
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 17.04
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.22 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 24.12 %
    Favored  : 75.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.35 (0.32), residues: 714
  helix:  1.26 (0.28), residues: 348
  sheet: -0.12 (0.54), residues: 105
  loop : -0.98 (0.39), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 181 
 TYR   0.018   0.001   TYR A 590 
 PHE   0.011   0.001   PHE A 175 
 TRP   0.010   0.001   TRP H  50 
 HIS   0.002   0.001   HIS A 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.02177 ( 5960)
  covalent geometry    : angle       0.94257 ( 8078)
  SS BOND              : bond        0.00460 (    8)
  SS BOND              : angle       0.55445 (   16)
  hydrogen bonds       : bond        0.16849 (  327)
  hydrogen bonds       : angle       6.63758 (  946)
  link_NAG-ASN         : bond        0.07217 (    1)
  link_NAG-ASN         : angle       5.68672 (    3)

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

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

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1428 Ramachandran restraints generated.
    714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 103
  time to evaluate  : 0.203 
Fit side-chains
REVERT: A  640 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.6864 (t80)
REVERT: H   21 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7055 (tp)
  outliers start: 5
  outliers final: 1
  residues processed: 107
  average time/residue: 0.3674
  time to fit residues: 41.8020
Evaluate side-chains
  91 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 88
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  640 TYR
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain L residue   55 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    8.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 469 GLN
A 476 ASN
** H  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   7 GLN
** L  90 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 = 0.3965 r_free = 0.3965 target = 0.164210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.138081 restraints weight = 20357.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.3667 rms_B_bonded: 2.80
r_work: 0.3528 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3527
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3527 r_free = 0.3527    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3527 r_free = 0.3527    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3527
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.1316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5969  Z= 0.153
  Angle     :  0.658   9.458   8097  Z= 0.323
  Chirality :  0.044   0.219    925
  Planarity :  0.004   0.048    969
  Dihedral  :  7.831  80.381   1009
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.09 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 21.73 %
    Favored  : 73.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.14 %
    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 aren not related in a simple way.
  whole:  0.70 (0.32), residues: 716
  helix:  1.62 (0.27), residues: 353
  sheet:  0.04 (0.53), residues: 108
  loop : -0.96 (0.39), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 181 
 TYR   0.020   0.001   TYR A 590 
 PHE   0.011   0.001   PHE A 175 
 TRP   0.007   0.001   TRP A 254 
 HIS   0.002   0.001   HIS A 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 5960)
  covalent geometry    : angle       0.65380 ( 8078)
  SS BOND              : bond        0.00320 (    8)
  SS BOND              : angle       0.82237 (   16)
  hydrogen bonds       : bond        0.04840 (  327)
  hydrogen bonds       : angle       5.00113 (  946)
  link_NAG-ASN         : bond        0.00450 (    1)
  link_NAG-ASN         : angle       3.74609 (    3)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 99
  time to evaluate  : 0.138 
Fit side-chains
REVERT: A  390 MET cc_start: 0.6234 (OUTLIER) cc_final: 0.5813 (ptm)
REVERT: A  446 ASN cc_start: 0.6113 (m-40) cc_final: 0.5900 (m-40)
REVERT: A  640 TYR cc_start: 0.7924 (OUTLIER) cc_final: 0.7380 (t80)
REVERT: H   21 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7264 (tp)
REVERT: L   67 ARG cc_start: 0.6309 (OUTLIER) cc_final: 0.5853 (ppt170)
  outliers start: 32
  outliers final: 11
  residues processed: 116
  average time/residue: 0.2778
  time to fit residues: 34.8102
Evaluate side-chains
  102 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  390 MET
Chi-restraints excluded: chain A residue  474 CYS
Chi-restraints excluded: chain A residue  553 THR
Chi-restraints excluded: chain A residue  563 VAL
Chi-restraints excluded: chain A residue  640 TYR
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   24 SER
Chi-restraints excluded: chain H residue   51 VAL
Chi-restraints excluded: chain L residue   11 SER
Chi-restraints excluded: chain L residue   67 ARG
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  104 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 43 optimal weight:    0.7980
   chunk 35 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9990
   chunk 50 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   chunk 7 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 72 optimal weight:    9.9990
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
L   7 GLN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 101 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.165261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.139400 restraints weight = 21617.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3709 rms_B_bonded: 2.93
r_work: 0.3567 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3567
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3567 r_free = 0.3567    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3567 r_free = 0.3567    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3567
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.1656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5969  Z= 0.131
  Angle     :  0.629  12.229   8097  Z= 0.304
  Chirality :  0.043   0.214    925
  Planarity :  0.004   0.043    969
  Dihedral  :  7.238  77.851   1007
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 22.84 %
    Favored  : 72.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.14 %
    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 aren not related in a simple way.
  whole:  0.83 (0.32), residues: 716
  helix:  1.82 (0.27), residues: 346
  sheet:  0.01 (0.51), residues: 110
  loop : -0.94 (0.39), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 181 
 TYR   0.021   0.001   TYR A 590 
 PHE   0.011   0.001   PHE A 175 
 TRP   0.006   0.001   TRP H  50 
 HIS   0.002   0.001   HIS A 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 5960)
  covalent geometry    : angle       0.62556 ( 8078)
  SS BOND              : bond        0.00290 (    8)
  SS BOND              : angle       0.67349 (   16)
  hydrogen bonds       : bond        0.04409 (  327)
  hydrogen bonds       : angle       4.70535 (  946)
  link_NAG-ASN         : bond        0.00099 (    1)
  link_NAG-ASN         : angle       3.47244 (    3)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 99
  time to evaluate  : 0.154 
Fit side-chains
REVERT: A  239 TYR cc_start: 0.6915 (m-10) cc_final: 0.5852 (m-10)
REVERT: A  446 ASN cc_start: 0.6303 (m-40) cc_final: 0.6085 (m-40)
REVERT: A  577 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7907 (tmt)
REVERT: A  640 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.7352 (t80)
REVERT: H   21 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7082 (tp)
REVERT: L   48 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.6982 (mt)
REVERT: L   67 ARG cc_start: 0.6341 (OUTLIER) cc_final: 0.5881 (ppt170)
  outliers start: 32
  outliers final: 12
  residues processed: 116
  average time/residue: 0.3357
  time to fit residues: 41.6635
Evaluate side-chains
  107 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  411 SER
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  563 VAL
Chi-restraints excluded: chain A residue  577 MET
Chi-restraints excluded: chain A residue  640 TYR
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   24 SER
Chi-restraints excluded: chain L residue   11 SER
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue   67 ARG
Chi-restraints excluded: chain L residue   97 ILE
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  104 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 0 optimal weight:    8.9990
   chunk 29 optimal weight:    0.9990
   chunk 16 optimal weight:    6.9990
   chunk 23 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 54 optimal weight:    9.9990
   chunk 67 optimal weight:    0.2980
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
H  80 ASN
** H  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   7 GLN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 101 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.165411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.140083 restraints weight = 17634.303|
|-----------------------------------------------------------------------------|
r_work (start): 0.3690 rms_B_bonded: 2.48
r_work: 0.3558 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3585
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3585 r_free = 0.3585    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3585 r_free = 0.3585    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3585
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.1786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5969  Z= 0.125
  Angle     :  0.622   9.276   8097  Z= 0.300
  Chirality :  0.043   0.216    925
  Planarity :  0.004   0.044    969
  Dihedral  :  6.960  69.524   1007
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 24.44 %
    Favored  : 71.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.14 %
    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 aren not related in a simple way.
  whole:  0.91 (0.32), residues: 716
  helix:  1.83 (0.28), residues: 346
  sheet:  0.22 (0.53), residues: 107
  loop : -0.89 (0.39), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 181 
 TYR   0.021   0.001   TYR A 590 
 PHE   0.011   0.001   PHE A 175 
 TRP   0.007   0.001   TRP H  50 
 HIS   0.002   0.001   HIS A 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 5960)
  covalent geometry    : angle       0.61719 ( 8078)
  SS BOND              : bond        0.00272 (    8)
  SS BOND              : angle       0.77829 (   16)
  hydrogen bonds       : bond        0.04231 (  327)
  hydrogen bonds       : angle       4.56055 (  946)
  link_NAG-ASN         : bond        0.00055 (    1)
  link_NAG-ASN         : angle       4.07143 (    3)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 98
  time to evaluate  : 0.204 
Fit side-chains
REVERT: A  239 TYR cc_start: 0.6973 (m-10) cc_final: 0.6130 (m-10)
REVERT: A  446 ASN cc_start: 0.6380 (m-40) cc_final: 0.6163 (m-40)
REVERT: A  640 TYR cc_start: 0.7886 (OUTLIER) cc_final: 0.7348 (t80)
REVERT: H   21 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.7035 (tp)
REVERT: L   48 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7097 (mt)
REVERT: L   67 ARG cc_start: 0.6315 (OUTLIER) cc_final: 0.5804 (ppt170)
  outliers start: 24
  outliers final: 13
  residues processed: 111
  average time/residue: 0.2984
  time to fit residues: 35.6928
Evaluate side-chains
  110 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  411 SER
Chi-restraints excluded: chain A residue  477 ASN
Chi-restraints excluded: chain A residue  505 SER
Chi-restraints excluded: chain A residue  563 VAL
Chi-restraints excluded: chain A residue  640 TYR
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   24 SER
Chi-restraints excluded: chain H residue   51 VAL
Chi-restraints excluded: chain L residue   11 SER
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue   67 ARG
Chi-restraints excluded: chain L residue   97 ILE
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  104 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   chunk 54 optimal weight:   10.0000
   chunk 25 optimal weight:    2.9990
   chunk 31 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 69 optimal weight:    9.9990
   chunk 17 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
H  80 ASN
** H  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   7 GLN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 101 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.163927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.138188 restraints weight = 14573.003|
|-----------------------------------------------------------------------------|
r_work (start): 0.3666 rms_B_bonded: 2.41
r_work: 0.3523 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3520
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3520 r_free = 0.3520    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3520 r_free = 0.3520    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3520
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.1951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5969  Z= 0.146
  Angle     :  0.660   8.645   8097  Z= 0.325
  Chirality :  0.044   0.221    925
  Planarity :  0.004   0.046    969
  Dihedral  :  7.015  60.185   1007
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 24.60 %
    Favored  : 71.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.14 %
    Twisted Proline : 4.35 %
    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 aren not related in a simple way.
  whole:  0.74 (0.32), residues: 716
  helix:  1.69 (0.28), residues: 346
  sheet:  0.33 (0.54), residues: 102
  loop : -1.04 (0.38), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 526 
 TYR   0.018   0.001   TYR A 590 
 PHE   0.012   0.001   PHE A 175 
 TRP   0.006   0.001   TRP A 254 
 HIS   0.004   0.001   HIS A 520 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 5960)
  covalent geometry    : angle       0.64771 ( 8078)
  SS BOND              : bond        0.00424 (    8)
  SS BOND              : angle       2.13366 (   16)
  hydrogen bonds       : bond        0.04545 (  327)
  hydrogen bonds       : angle       4.62110 (  946)
  link_NAG-ASN         : bond        0.00053 (    1)
  link_NAG-ASN         : angle       4.64826 (    3)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 100
  time to evaluate  : 0.202 
Fit side-chains
REVERT: A  446 ASN cc_start: 0.6501 (m-40) cc_final: 0.6221 (m110)
REVERT: A  640 TYR cc_start: 0.7936 (OUTLIER) cc_final: 0.7283 (t80)
REVERT: H   21 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.7032 (tp)
REVERT: L   48 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7184 (mt)
REVERT: L   67 ARG cc_start: 0.6356 (OUTLIER) cc_final: 0.5755 (ppt170)
  outliers start: 26
  outliers final: 15
  residues processed: 114
  average time/residue: 0.3534
  time to fit residues: 42.9208
Evaluate side-chains
  113 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  104 MET
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  411 SER
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  505 SER
Chi-restraints excluded: chain A residue  563 VAL
Chi-restraints excluded: chain A residue  640 TYR
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   24 SER
Chi-restraints excluded: chain H residue   51 VAL
Chi-restraints excluded: chain L residue   11 SER
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue   67 ARG
Chi-restraints excluded: chain L residue   97 ILE
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  104 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 59 optimal weight:    7.9990
   chunk 9 optimal weight:    0.0070
   chunk 72 optimal weight:    9.9990
   chunk 53 optimal weight:    7.9990
   chunk 14 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 67 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   overall best weight:    1.0802

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

Flipped N/Q/H residues before XYZ refinement:
H  80 ASN
** H  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   7 GLN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 101 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.163529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.137903 restraints weight = 23361.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.3691 rms_B_bonded: 3.39
r_work: 0.3531 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3530
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3530 r_free = 0.3530    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3530 r_free = 0.3530    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3530
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.2094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5969  Z= 0.142
  Angle     :  0.648   7.952   8097  Z= 0.318
  Chirality :  0.043   0.222    925
  Planarity :  0.004   0.046    969
  Dihedral  :  6.674  58.758   1007
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 25.88 %
    Favored  : 69.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.14 %
    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 aren not related in a simple way.
  whole:  0.74 (0.32), residues: 716
  helix:  1.69 (0.28), residues: 346
  sheet:  0.36 (0.54), residues: 102
  loop : -1.06 (0.38), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 526 
 TYR   0.019   0.001   TYR A 590 
 PHE   0.013   0.001   PHE A  73 
 TRP   0.006   0.001   TRP H  50 
 HIS   0.003   0.001   HIS A 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 5960)
  covalent geometry    : angle       0.63605 ( 8078)
  SS BOND              : bond        0.00262 (    8)
  SS BOND              : angle       1.60364 (   16)
  hydrogen bonds       : bond        0.04487 (  327)
  hydrogen bonds       : angle       4.60526 (  946)
  link_NAG-ASN         : bond        0.00076 (    1)
  link_NAG-ASN         : angle       5.41228 (    3)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 100
  time to evaluate  : 0.169 
Fit side-chains
REVERT: A  640 TYR cc_start: 0.7941 (OUTLIER) cc_final: 0.7284 (t80)
REVERT: H   21 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.6958 (tp)
REVERT: L   48 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7184 (mt)
REVERT: L   67 ARG cc_start: 0.6313 (OUTLIER) cc_final: 0.5937 (ppt170)
  outliers start: 26
  outliers final: 13
  residues processed: 113
  average time/residue: 0.3282
  time to fit residues: 39.7740
Evaluate side-chains
  112 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 95
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  411 SER
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  505 SER
Chi-restraints excluded: chain A residue  563 VAL
Chi-restraints excluded: chain A residue  640 TYR
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   24 SER
Chi-restraints excluded: chain H residue   51 VAL
Chi-restraints excluded: chain L residue   11 SER
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue   67 ARG
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  104 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 64 optimal weight:    0.8980
   chunk 60 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 69 optimal weight:    0.0980
   chunk 63 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0570
   chunk 5 optimal weight:    0.9990
   chunk 57 optimal weight:    4.9990
   chunk 56 optimal weight:    0.6980
   overall best weight:    0.4698

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

Flipped N/Q/H residues before XYZ refinement:
A 544 ASN
H  80 ASN
** H  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  90 GLN
L 101 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.168550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.143019 restraints weight = 21522.134|
|-----------------------------------------------------------------------------|
r_work (start): 0.3751 rms_B_bonded: 2.79
r_work: 0.3593 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3592
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3592 r_free = 0.3592    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3592 r_free = 0.3592    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3592
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.2276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5969  Z= 0.114
  Angle     :  0.604   7.739   8097  Z= 0.295
  Chirality :  0.042   0.214    925
  Planarity :  0.004   0.044    969
  Dihedral  :  6.127  59.231   1007
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 26.36 %
    Favored  : 69.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.14 %
    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 aren not related in a simple way.
  whole:  0.92 (0.32), residues: 716
  helix:  1.87 (0.28), residues: 346
  sheet:  0.41 (0.53), residues: 102
  loop : -0.99 (0.38), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 526 
 TYR   0.022   0.001   TYR A 590 
 PHE   0.012   0.001   PHE A 175 
 TRP   0.009   0.001   TRP H  50 
 HIS   0.003   0.001   HIS A 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 5960)
  covalent geometry    : angle       0.59416 ( 8078)
  SS BOND              : bond        0.00320 (    8)
  SS BOND              : angle       1.12292 (   16)
  hydrogen bonds       : bond        0.03879 (  327)
  hydrogen bonds       : angle       4.37139 (  946)
  link_NAG-ASN         : bond        0.00023 (    1)
  link_NAG-ASN         : angle       5.35768 (    3)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 101
  time to evaluate  : 0.228 
Fit side-chains
REVERT: A   83 PHE cc_start: 0.6878 (m-10) cc_final: 0.6508 (m-80)
REVERT: A  596 ASP cc_start: 0.7575 (m-30) cc_final: 0.7361 (m-30)
REVERT: A  640 TYR cc_start: 0.7809 (OUTLIER) cc_final: 0.7374 (t80)
REVERT: H   21 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6942 (tp)
REVERT: L   48 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7175 (mt)
REVERT: L   67 ARG cc_start: 0.6317 (OUTLIER) cc_final: 0.5780 (ppt170)
  outliers start: 25
  outliers final: 11
  residues processed: 115
  average time/residue: 0.2977
  time to fit residues: 36.8667
Evaluate side-chains
  109 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  411 SER
Chi-restraints excluded: chain A residue  505 SER
Chi-restraints excluded: chain A residue  563 VAL
Chi-restraints excluded: chain A residue  640 TYR
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   51 VAL
Chi-restraints excluded: chain H residue  129 THR
Chi-restraints excluded: chain L residue   11 SER
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue   67 ARG
Chi-restraints excluded: chain L residue   97 ILE
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 54 optimal weight:    5.9990
   chunk 37 optimal weight:    7.9990
   chunk 63 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9980
   chunk 51 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
H  80 ASN
** H  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 101 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.165146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.139118 restraints weight = 20838.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.3699 rms_B_bonded: 2.86
r_work: 0.3553 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3554
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3554 r_free = 0.3554    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3554 r_free = 0.3554    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3554
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5969  Z= 0.135
  Angle     :  0.638   9.334   8097  Z= 0.311
  Chirality :  0.042   0.220    925
  Planarity :  0.004   0.046    969
  Dihedral  :  6.175  59.486   1007
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 25.88 %
    Favored  : 70.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.14 %
    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 aren not related in a simple way.
  whole:  0.82 (0.32), residues: 716
  helix:  1.77 (0.28), residues: 347
  sheet:  0.35 (0.52), residues: 108
  loop : -1.06 (0.39), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 580 
 TYR   0.018   0.001   TYR A 590 
 PHE   0.013   0.001   PHE A 175 
 TRP   0.006   0.001   TRP A 254 
 HIS   0.003   0.001   HIS A 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 5960)
  covalent geometry    : angle       0.62898 ( 8078)
  SS BOND              : bond        0.00323 (    8)
  SS BOND              : angle       1.03052 (   16)
  hydrogen bonds       : bond        0.04310 (  327)
  hydrogen bonds       : angle       4.49177 (  946)
  link_NAG-ASN         : bond        0.00061 (    1)
  link_NAG-ASN         : angle       5.19036 (    3)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 96
  time to evaluate  : 0.185 
Fit side-chains
REVERT: A   83 PHE cc_start: 0.6859 (m-10) cc_final: 0.6531 (m-80)
REVERT: A  640 TYR cc_start: 0.7951 (OUTLIER) cc_final: 0.7262 (t80)
REVERT: A  650 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7947 (mptm)
REVERT: H   21 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6951 (tp)
REVERT: L   48 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7155 (mt)
REVERT: L   67 ARG cc_start: 0.6257 (OUTLIER) cc_final: 0.5803 (ppt170)
  outliers start: 25
  outliers final: 14
  residues processed: 112
  average time/residue: 0.3298
  time to fit residues: 39.7183
Evaluate side-chains
  113 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  411 SER
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  505 SER
Chi-restraints excluded: chain A residue  563 VAL
Chi-restraints excluded: chain A residue  618 SER
Chi-restraints excluded: chain A residue  640 TYR
Chi-restraints excluded: chain A residue  650 LYS
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue  119 LEU
Chi-restraints excluded: chain H residue  129 THR
Chi-restraints excluded: chain L residue   11 SER
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue   67 ARG
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  104 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 11 optimal weight:    0.5980
   chunk 38 optimal weight:    5.9990
   chunk 40 optimal weight:    0.7980
   chunk 13 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 70 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
H  80 ASN
** H  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   7 GLN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 101 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.165796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.140147 restraints weight = 15537.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3715 rms_B_bonded: 2.31
r_work: 0.3570 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3570
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3570 r_free = 0.3570    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3570 r_free = 0.3570    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3570
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.2372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5969  Z= 0.130
  Angle     :  0.628   8.424   8097  Z= 0.308
  Chirality :  0.042   0.219    925
  Planarity :  0.004   0.045    969
  Dihedral  :  5.989  59.062   1007
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 26.68 %
    Favored  : 69.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.14 %
    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 aren not related in a simple way.
  whole:  0.82 (0.32), residues: 716
  helix:  1.75 (0.28), residues: 347
  sheet:  0.38 (0.52), residues: 108
  loop : -1.05 (0.39), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  62 
 TYR   0.019   0.001   TYR A 590 
 PHE   0.012   0.001   PHE A 175 
 TRP   0.008   0.001   TRP H  50 
 HIS   0.003   0.001   HIS A 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 5960)
  covalent geometry    : angle       0.62079 ( 8078)
  SS BOND              : bond        0.00335 (    8)
  SS BOND              : angle       0.97818 (   16)
  hydrogen bonds       : bond        0.04204 (  327)
  hydrogen bonds       : angle       4.48287 (  946)
  link_NAG-ASN         : bond        0.00022 (    1)
  link_NAG-ASN         : angle       4.64089 (    3)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 100
  time to evaluate  : 0.231 
Fit side-chains
REVERT: A   83 PHE cc_start: 0.6918 (m-10) cc_final: 0.6603 (m-80)
REVERT: A  180 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.6896 (mm)
REVERT: A  640 TYR cc_start: 0.7897 (OUTLIER) cc_final: 0.7312 (t80)
REVERT: H   21 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6947 (tp)
REVERT: L   48 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7231 (mt)
  outliers start: 23
  outliers final: 15
  residues processed: 117
  average time/residue: 0.3247
  time to fit residues: 40.8774
Evaluate side-chains
  115 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  411 SER
Chi-restraints excluded: chain A residue  505 SER
Chi-restraints excluded: chain A residue  563 VAL
Chi-restraints excluded: chain A residue  618 SER
Chi-restraints excluded: chain A residue  640 TYR
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   24 SER
Chi-restraints excluded: chain H residue   51 VAL
Chi-restraints excluded: chain H residue  119 LEU
Chi-restraints excluded: chain H residue  129 THR
Chi-restraints excluded: chain L residue   11 SER
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue   67 ARG
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  104 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 30 optimal weight:    0.5980
   chunk 49 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   chunk 37 optimal weight:   10.0000
   chunk 71 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 46 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
H  80 ASN
** H  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   7 GLN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 101 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.165289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.139689 restraints weight = 20082.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.3711 rms_B_bonded: 2.79
r_work: 0.3569 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3563
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3563 r_free = 0.3563    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3563 r_free = 0.3563    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3563
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.2371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5969  Z= 0.130
  Angle     :  0.627   8.503   8097  Z= 0.309
  Chirality :  0.042   0.219    925
  Planarity :  0.004   0.046    969
  Dihedral  :  5.957  58.632   1007
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 26.20 %
    Favored  : 69.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.14 %
    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 aren not related in a simple way.
  whole:  0.80 (0.32), residues: 716
  helix:  1.74 (0.28), residues: 347
  sheet:  0.41 (0.53), residues: 108
  loop : -1.07 (0.39), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 526 
 TYR   0.019   0.001   TYR A 590 
 PHE   0.012   0.001   PHE A 175 
 TRP   0.010   0.001   TRP H  50 
 HIS   0.003   0.001   HIS A 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 5960)
  covalent geometry    : angle       0.62101 ( 8078)
  SS BOND              : bond        0.00407 (    8)
  SS BOND              : angle       0.95563 (   16)
  hydrogen bonds       : bond        0.04230 (  327)
  hydrogen bonds       : angle       4.47843 (  946)
  link_NAG-ASN         : bond        0.00008 (    1)
  link_NAG-ASN         : angle       4.34835 (    3)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 100
  time to evaluate  : 0.173 
Fit side-chains
REVERT: A   83 PHE cc_start: 0.6851 (m-10) cc_final: 0.6574 (m-80)
REVERT: A  180 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.6834 (mm)
REVERT: A  596 ASP cc_start: 0.7667 (m-30) cc_final: 0.7391 (m-30)
REVERT: A  640 TYR cc_start: 0.7911 (OUTLIER) cc_final: 0.7290 (t80)
REVERT: H   21 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.6899 (tp)
REVERT: L   48 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7190 (mt)
REVERT: L  104 LYS cc_start: 0.7488 (OUTLIER) cc_final: 0.7126 (pttt)
  outliers start: 26
  outliers final: 16
  residues processed: 116
  average time/residue: 0.3338
  time to fit residues: 41.8867
Evaluate side-chains
  117 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  411 SER
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  505 SER
Chi-restraints excluded: chain A residue  563 VAL
Chi-restraints excluded: chain A residue  618 SER
Chi-restraints excluded: chain A residue  640 TYR
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   24 SER
Chi-restraints excluded: chain H residue   51 VAL
Chi-restraints excluded: chain H residue  119 LEU
Chi-restraints excluded: chain H residue  129 THR
Chi-restraints excluded: chain L residue   11 SER
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue   67 ARG
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  104 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 55 optimal weight:    0.2980
   chunk 1 optimal weight:    3.9990
   chunk 40 optimal weight:    0.6980
   chunk 59 optimal weight:    4.9990
   chunk 64 optimal weight:    4.9990
   chunk 6 optimal weight:    9.9990
   chunk 48 optimal weight:    4.9990
   chunk 8 optimal weight:    0.0770
   chunk 35 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    1.2142

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

Flipped N/Q/H residues before XYZ refinement:
A 169 HIS
H  80 ASN
** H  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   7 GLN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 101 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.163088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.137245 restraints weight = 18481.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3654 rms_B_bonded: 2.54
r_work: 0.3521 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3540
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3540 r_free = 0.3540    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3540 r_free = 0.3540    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3540
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.2422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5969  Z= 0.150
  Angle     :  0.655   8.398   8097  Z= 0.325
  Chirality :  0.043   0.225    925
  Planarity :  0.004   0.046    969
  Dihedral  :  6.132  58.535   1007
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 26.36 %
    Favored  : 69.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.14 %
    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 aren not related in a simple way.
  whole:  0.68 (0.32), residues: 716
  helix:  1.62 (0.28), residues: 346
  sheet:  0.39 (0.53), residues: 108
  loop : -1.11 (0.39), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 526 
 TYR   0.016   0.001   TYR A 590 
 PHE   0.014   0.001   PHE A  73 
 TRP   0.009   0.001   TRP H  50 
 HIS   0.004   0.001   HIS A 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 5960)
  covalent geometry    : angle       0.64973 ( 8078)
  SS BOND              : bond        0.00408 (    8)
  SS BOND              : angle       0.98140 (   16)
  hydrogen bonds       : bond        0.04581 (  327)
  hydrogen bonds       : angle       4.61146 (  946)
  link_NAG-ASN         : bond        0.00042 (    1)
  link_NAG-ASN         : angle       4.08309 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2141.91 seconds
wall clock time: 37 minutes 16.78 seconds (2236.78 seconds total)