Starting phenix.real_space_refine
on Tue Mar  3 15:43:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lsz_63360/03_2026/9lsz_63360.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lsz_63360/03_2026/9lsz_63360.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.11
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lsz_63360/03_2026/9lsz_63360.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lsz_63360/03_2026/9lsz_63360.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lsz_63360/03_2026/9lsz_63360.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lsz_63360/03_2026/9lsz_63360.map"
  }
  resolution = 3.11
  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=   0.002
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      35      5.16       5
     C    4237      2.51       5
     N    1005      2.21       5
     O    1181      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6458
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4620
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 583, 4620
          Classifications: {'peptide': 583}
          Link IDs: {'PTRANS': 28, 'TRANS': 554}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "L"
      Number of atoms: 848
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 848
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 4, 'TRANS': 105}
    Chain: "H"
      Number of atoms: 962
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 962
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 4, 'TRANS': 115}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 1.39, per 1000 atoms: 0.22
  Number of scatterers: 6458
  At special positions: 0
  Unit cell: (74.7, 75.53, 139.44, 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      35     16.00
     O    1181      8.00
     N    1005      7.00
     C    4237      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 153 " - pdb=" SG  CYS A 166 " distance=2.07
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 383 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  32 " - pdb=" SG  CYS L 103 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  30 " - pdb=" SG  CYS H 104 " distance=2.01

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
    NAG-ASN
      " NAG B   1 " - " ASN A 258 "
  Time building additional restraints: 0.62
  Conformation dependent library (CDL) restraints added in 208.1 milliseconds
  

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1506

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 6 sheets defined
      59.9% alpha, 9.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 26
    Processing helix  chain 'A' and resid 40 through 48
      removed outlier: 3.597A  pdb=" N   CYS A  45 " --> pdb=" O   TYR A  41 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   PHE A  48 " --> pdb=" O   THR A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 56
    Processing helix  chain 'A' and resid 56 through 64
      removed outlier: 3.985A  pdb=" N   TYR A  60 " --> pdb=" O   TRP A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 81
      Proline residue:  A  73  - end of helix
    Processing helix  chain 'A' and resid 81 through 97
    Processing helix  chain 'A' and resid 99 through 108
      removed outlier: 3.775A  pdb=" N   TRP A 104 " --> pdb=" O   SER A 100 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   SER A 105 " --> pdb=" O   LEU A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 111
      No H-bonds generated for 'chain 'A' and resid 109 through 111'
    Processing helix  chain 'A' and resid 112 through 142
      removed outlier: 4.075A  pdb=" N   TYR A 128 " --> pdb=" O   MET A 124 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   THR A 131 " --> pdb=" O   LEU A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 169
    Processing helix  chain 'A' and resid 170 through 178
    Processing helix  chain 'A' and resid 194 through 212
    Processing helix  chain 'A' and resid 215 through 227
      removed outlier: 4.060A  pdb=" N   GLY A 220 " --> pdb=" O   ILE A 216 " (cutoff:3.500A)
      removed outlier: 5.252A  pdb=" N   TYR A 224 " --> pdb=" O   GLY A 220 " (cutoff:3.500A)
      removed outlier: 5.636A  pdb=" N   ILE A 225 " --> pdb=" O   LYS A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 243
    Processing helix  chain 'A' and resid 246 through 256
      removed outlier: 3.532A  pdb=" N   PHE A 255 " --> pdb=" O   ILE A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 263
    Processing helix  chain 'A' and resid 264 through 280
      removed outlier: 3.569A  pdb=" N   TRP A 268 " --> pdb=" O   GLN A 264 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   PHE A 276 " --> pdb=" O   GLY A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 291
    Processing helix  chain 'A' and resid 298 through 348
      removed outlier: 3.518A  pdb=" N   ASP A 302 " --> pdb=" O   ASN A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 371
    Processing helix  chain 'A' and resid 371 through 377
    Processing helix  chain 'A' and resid 384 through 391
    Processing helix  chain 'A' and resid 397 through 409
    Processing helix  chain 'A' and resid 412 through 447
      removed outlier: 3.765A  pdb=" N   TRP A 416 " --> pdb=" O   LEU A 412 " (cutoff:3.500A)
      Proline residue:  A 442  - end of helix
    Processing helix  chain 'A' and resid 454 through 475
      removed outlier: 3.574A  pdb=" N   LEU A 458 " --> pdb=" O   PRO A 454 " (cutoff:3.500A)
      removed outlier: 4.581A  pdb=" N   ILE A 472 " --> pdb=" O   LEU A 468 " (cutoff:3.500A)
      removed outlier: 4.688A  pdb=" N   PHE A 473 " --> pdb=" O   ILE A 469 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   THR A 474 " --> pdb=" O   GLY A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 477 through 490
      removed outlier: 3.719A  pdb=" N   GLY A 490 " --> pdb=" O   ASP A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 508
    Processing helix  chain 'A' and resid 510 through 523
    Processing helix  chain 'A' and resid 527 through 536
    Processing helix  chain 'A' and resid 536 through 554
      removed outlier: 3.507A  pdb=" N   PHE A 550 " --> pdb=" O   PHE A 546 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   VAL A 554 " --> pdb=" O   PHE A 550 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 590
      removed outlier: 3.709A  pdb=" N   VAL A 585 " --> pdb=" O   TRP A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 591 through 608
      removed outlier: 4.152A  pdb=" N   ILE A 597 " --> pdb=" O   PRO A 593 " (cutoff:3.500A)
      Proline residue:  A 598  - end of helix
    Processing helix  chain 'L' and resid 94 through 98
      removed outlier: 4.031A  pdb=" N   LEU L  98 " --> pdb=" O   ALA L  95 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 36 through 40
      removed outlier: 3.507A  pdb=" N   TYR H  40 " --> pdb=" O   PHE H  37 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 70 through 73
    Processing helix  chain 'H' and resid 82 through 85
    Processing sheet with id=AA1, first strand: chain 'A' and resid 559 through 562
      removed outlier: 4.080A  pdb=" N   GLN A 574 " --> pdb=" O   ILE A 562 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'L' and resid 13 through 14
    Processing sheet with id=AA3, first strand: chain 'L' and resid 19 through 21
      removed outlier: 3.721A  pdb=" N   THR L 116 " --> pdb=" O   TYR L 101 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   TYR L 102 " --> pdb=" O   TYR L  51 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 39 through 40
    Processing sheet with id=AA5, first strand: chain 'H' and resid 18 through 19
      removed outlier: 6.642A  pdb=" N   GLU H  18 " --> pdb=" O   THR H 128 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   ILE H  42 " --> pdb=" O   TRP H  58 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   TRP H  58 " --> pdb=" O   ILE H  42 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   TRP H  44 " --> pdb=" O   ILE H  56 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 26 through 29
      removed outlier: 3.524A  pdb=" N   VAL H  26 " --> pdb=" O   LEU H  91 " (cutoff:3.500A)

    364 hydrogen bonds defined for protein.
    1059 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: 1.16

  Time building geometry restraints manager: 0.78 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1017
        1.31 -     1.44: 1938
        1.44 -     1.57: 3631
        1.57 -     1.70: 0
        1.70 -     1.83: 52
  Bond restraints: 6638
  Sorted by residual:
  bond pdb=" C   ASP A 384 "
       pdb=" O   ASP A 384 "
    ideal  model  delta    sigma   weight residual
    1.235  1.304 -0.069 1.19e-02 7.06e+03 3.39e+01
  bond pdb=" C   VAL A 393 "
       pdb=" O   VAL A 393 "
    ideal  model  delta    sigma   weight residual
    1.235  1.185  0.049 1.02e-02 9.61e+03 2.35e+01
  bond pdb=" C   GLY A 395 "
       pdb=" O   GLY A 395 "
    ideal  model  delta    sigma   weight residual
    1.236  1.192  0.045 1.02e-02 9.61e+03 1.92e+01
  bond pdb=" N   THR A 356 "
       pdb=" CA  THR A 356 "
    ideal  model  delta    sigma   weight residual
    1.454  1.503 -0.049 1.17e-02 7.31e+03 1.77e+01
  bond pdb=" CA  SER A 323 "
       pdb=" CB  SER A 323 "
    ideal  model  delta    sigma   weight residual
    1.530  1.465  0.065 1.56e-02 4.11e+03 1.72e+01
  ... (remaining 6633 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.50: 5243
        1.50 -     3.00: 2801
        3.00 -     4.50: 900
        4.50 -     6.00: 97
        6.00 -     7.49: 11
  Bond angle restraints: 9052
  Sorted by residual:
  angle pdb=" C   THR A 256 "
        pdb=" CA  THR A 256 "
        pdb=" CB  THR A 256 "
      ideal   model   delta    sigma   weight residual
     110.44  115.95   -5.51 9.00e-01 1.23e+00 3.75e+01
  angle pdb=" CA  GLY H 124 "
        pdb=" C   GLY H 124 "
        pdb=" O   GLY H 124 "
      ideal   model   delta    sigma   weight residual
     122.22  118.36    3.86 6.50e-01 2.37e+00 3.52e+01
  angle pdb=" CA  ILE A 239 "
        pdb=" C   ILE A 239 "
        pdb=" O   ILE A 239 "
      ideal   model   delta    sigma   weight residual
     121.17  115.01    6.16 1.06e+00 8.90e-01 3.37e+01
  angle pdb=" CA  GLY A 395 "
        pdb=" C   GLY A 395 "
        pdb=" O   GLY A 395 "
      ideal   model   delta    sigma   weight residual
     121.30  115.92    5.38 9.80e-01 1.04e+00 3.02e+01
  angle pdb=" C   SER A 491 "
        pdb=" N   ILE A 492 "
        pdb=" CA  ILE A 492 "
      ideal   model   delta    sigma   weight residual
     120.33  124.57   -4.24 8.00e-01 1.56e+00 2.81e+01
  ... (remaining 9047 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.87: 3513
       17.87 -    35.75: 259
       35.75 -    53.62: 51
       53.62 -    71.49: 30
       71.49 -    89.37: 5
  Dihedral angle restraints: 3858
    sinusoidal: 1498
      harmonic: 2360
  Sorted by residual:
  dihedral pdb=" CB  CYS A 336 "
           pdb=" SG  CYS A 336 "
           pdb=" SG  CYS A 383 "
           pdb=" CB  CYS A 383 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -177.63  -89.37     1      1.00e+01 1.00e-02 9.49e+01
  dihedral pdb=" CA  PRO A 257 "
           pdb=" C   PRO A 257 "
           pdb=" N   ASN A 258 "
           pdb=" CA  ASN A 258 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.07   19.93     0      5.00e+00 4.00e-02 1.59e+01
  dihedral pdb=" CA  GLY A  93 "
           pdb=" C   GLY A  93 "
           pdb=" N   GLN A  94 "
           pdb=" CA  GLN A  94 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.52   17.48     0      5.00e+00 4.00e-02 1.22e+01
  ... (remaining 3855 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 476
       0.055 -    0.110: 354
       0.110 -    0.165: 160
       0.165 -    0.220: 35
       0.220 -    0.275: 3
  Chirality restraints: 1028
  Sorted by residual:
  chirality pdb=" C1  NAG B   2 "
            pdb=" O4  NAG B   1 "
            pdb=" C2  NAG B   2 "
            pdb=" O5  NAG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.29   -0.11 2.00e-02 2.50e+03 3.12e+01
  chirality pdb=" CG  LEU L 110 "
            pdb=" CB  LEU L 110 "
            pdb=" CD1 LEU L 110 "
            pdb=" CD2 LEU L 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.31   -0.28 2.00e-01 2.50e+01 1.89e+00
  chirality pdb=" CB  VAL H  80 "
            pdb=" CA  VAL H  80 "
            pdb=" CG1 VAL H  80 "
            pdb=" CG2 VAL H  80 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.25 2.00e-01 2.50e+01 1.55e+00
  ... (remaining 1025 not shown)

  Planarity restraints: 1116
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 104 "   -0.030 2.00e-02 2.50e+03   1.39e-02 4.80e+00
        pdb=" CG  TRP A 104 "    0.019 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 104 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 104 "    0.014 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 104 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 104 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 104 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 104 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 104 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 104 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP A  56 "    0.011 2.00e-02 2.50e+03   2.18e-02 4.76e+00
        pdb=" C   TRP A  56 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   TRP A  56 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ARG A  57 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 176 "    0.016 2.00e-02 2.50e+03   1.34e-02 4.49e+00
        pdb=" CG  TRP A 176 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 176 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 176 "    0.010 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 176 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 176 "    0.023 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 176 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 176 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 176 "   -0.009 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 176 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1113 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 1865
        2.86 -     3.37: 7086
        3.37 -     3.88: 11547
        3.88 -     4.39: 13421
        4.39 -     4.90: 21590
  Nonbonded interactions: 55509
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN A 377 "
            pdb=" O   TYR L 108 "
     model   vdw
     2.349 3.120
  nonbonded pdb=" O   PHE A 400 "
            pdb=" OG1 THR A 404 "
     model   vdw
     2.403 3.040
  nonbonded pdb=" OD1 ASP H  39 "
            pdb=" NH2 ARG H  62 "
     model   vdw
     2.427 3.120
  nonbonded pdb=" O   LEU A 471 "
            pdb=" OG1 THR A 474 "
     model   vdw
     2.429 3.040
  nonbonded pdb=" O   PHE A 175 "
            pdb=" OG1 THR A 180 "
     model   vdw
     2.439 3.040
  ... (remaining 55504 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             4.540
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.650
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
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      :  0.015   0.071   6644  Z= 1.091
  Angle     :  1.869  15.494   9066  Z= 1.393
  Chirality :  0.082   0.275   1028
  Planarity :  0.005   0.025   1115
  Dihedral  : 14.398  78.702   2340
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.45 %
    Favored  : 91.43 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  :  7.33 %
    Favored  : 87.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.67 (0.23), residues: 805
  helix: -3.10 (0.18), residues: 423
  sheet: -2.63 (0.45), residues: 106
  loop : -2.90 (0.30), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 240 
 TYR   0.025   0.004   TYR A 128 
 PHE   0.016   0.004   PHE A 253 
 TRP   0.030   0.005   TRP A 104 
 HIS   0.007   0.003   HIS A 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.01481 ( 6638)
  covalent geometry    : angle       1.85873 ( 9052)
  SS BOND              : bond        0.02199 (    4)
  SS BOND              : angle       3.79221 (    8)
  hydrogen bonds       : bond        0.21401 (  364)
  hydrogen bonds       : angle       9.65320 ( 1059)
  link_BETA1-4         : bond        0.04376 (    1)
  link_BETA1-4         : angle       9.13620 (    3)
  link_NAG-ASN         : bond        0.01647 (    1)
  link_NAG-ASN         : angle       3.38080 (    3)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 164
  time to evaluate  : 0.205 
Fit side-chains
TARDY: cannot create tardy model for: "CYS A 383 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A   71 MET cc_start: 0.8287 (tpp) cc_final: 0.7962 (tpt)
REVERT: A   98 ARG cc_start: 0.7200 (mtt-85) cc_final: 0.6853 (mtm-85)
REVERT: A  210 MET cc_start: 0.5479 (mmm) cc_final: 0.5209 (mtt)
REVERT: A  245 LYS cc_start: 0.7458 (mttt) cc_final: 0.7128 (tttm)
REVERT: A  358 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8066 (tm-30)
REVERT: A  391 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7581 (mm-30)
REVERT: A  553 GLU cc_start: 0.6320 (tt0) cc_final: 0.6061 (tp30)
REVERT: A  557 GLU cc_start: 0.6882 (mt-10) cc_final: 0.6645 (pt0)
REVERT: A  568 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7406 (pt0)
REVERT: L   26 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7279 (tm-30)
REVERT: L   32 CYS cc_start: 0.7304 (t) cc_final: 0.6638 (t)
REVERT: L   46 ASN cc_start: 0.7228 (m-40) cc_final: 0.6936 (t0)
REVERT: L   64 TYR cc_start: 0.6951 (p90) cc_final: 0.6728 (p90)
REVERT: H   20 VAL cc_start: 0.7674 (OUTLIER) cc_final: 0.7047 (m)
REVERT: H   67 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7522 (mmtm)
REVERT: H   75 LYS cc_start: 0.7271 (tttt) cc_final: 0.6947 (tttp)
REVERT: H   90 GLN cc_start: 0.7739 (tt0) cc_final: 0.7113 (tm-30)
REVERT: H  114 ASP cc_start: 0.7999 (p0) cc_final: 0.7152 (p0)
  outliers start: 34
  outliers final: 10
  residues processed: 188
  average time/residue: 0.0953
  time to fit residues: 22.8127
Evaluate side-chains
  110 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   60 TYR
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  129 TYR
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  383 CYS
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain H residue   20 VAL
Chi-restraints excluded: chain H residue   67 LYS
Chi-restraints excluded: chain H residue  110 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.4980
   chunk 45 optimal weight:    0.6980
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  94 GLN
** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 145 GLN
A 249 ASN
A 293 ASN
A 524 HIS
A 527 ASN
A 574 GLN
L  52 GLN
H  47 GLN
H  90 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.153899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.109863 restraints weight = 7471.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 2.18
r_work: 0.3069 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2910 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.2595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6644  Z= 0.153
  Angle     :  0.638   7.228   9066  Z= 0.330
  Chirality :  0.043   0.173   1028
  Planarity :  0.004   0.027   1115
  Dihedral  :  6.729  58.390    937
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 11.00 %
    Favored  : 86.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.29 (0.27), residues: 805
  helix:  0.10 (0.23), residues: 439
  sheet: -1.74 (0.45), residues: 110
  loop : -1.96 (0.33), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 240 
 TYR   0.021   0.002   TYR A 316 
 PHE   0.024   0.002   PHE H 107 
 TRP   0.011   0.001   TRP A 104 
 HIS   0.004   0.002   HIS A  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 6638)
  covalent geometry    : angle       0.63608 ( 9052)
  SS BOND              : bond        0.00212 (    4)
  SS BOND              : angle       0.90227 (    8)
  hydrogen bonds       : bond        0.05398 (  364)
  hydrogen bonds       : angle       5.48151 ( 1059)
  link_BETA1-4         : bond        0.00306 (    1)
  link_BETA1-4         : angle       2.25039 (    3)
  link_NAG-ASN         : bond        0.00680 (    1)
  link_NAG-ASN         : angle       1.59908 (    3)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.241 
Fit side-chains
TARDY: cannot create tardy model for: "CYS A 383 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A  194 GLN cc_start: 0.7970 (mm110) cc_final: 0.7593 (mm110)
REVERT: A  391 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7229 (mm-30)
REVERT: L   26 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7397 (tm-30)
REVERT: L   32 CYS cc_start: 0.6831 (t) cc_final: 0.6161 (t)
REVERT: H   58 TRP cc_start: 0.9466 (OUTLIER) cc_final: 0.8714 (p90)
REVERT: H   67 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8204 (mmtm)
REVERT: H   75 LYS cc_start: 0.7924 (tttt) cc_final: 0.7589 (tttp)
REVERT: H   90 GLN cc_start: 0.8262 (tt0) cc_final: 0.7549 (tm-30)
REVERT: H  114 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.7317 (p0)
  outliers start: 19
  outliers final: 9
  residues processed: 126
  average time/residue: 0.0686
  time to fit residues: 11.9123
Evaluate side-chains
  105 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   60 TYR
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  383 CYS
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain L residue   14 THR
Chi-restraints excluded: chain L residue   43 THR
Chi-restraints excluded: chain H residue   58 TRP
Chi-restraints excluded: chain H residue   67 LYS
Chi-restraints excluded: chain H residue  114 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0070
   chunk 79 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 3 optimal weight:    0.6980
   chunk 56 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0870
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 296 HIS
** L  46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.150281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.105671 restraints weight = 7606.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.3137 rms_B_bonded: 2.21
r_work: 0.2995 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2843 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.3384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6644  Z= 0.156
  Angle     :  0.589   6.598   9066  Z= 0.305
  Chirality :  0.041   0.150   1028
  Planarity :  0.004   0.033   1115
  Dihedral  :  6.075  59.798    932
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 11.14 %
    Favored  : 86.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.14 (0.29), residues: 805
  helix:  1.07 (0.24), residues: 439
  sheet: -1.25 (0.45), residues: 127
  loop : -1.52 (0.37), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 240 
 TYR   0.020   0.002   TYR A 322 
 PHE   0.027   0.002   PHE A 546 
 TRP   0.011   0.001   TRP H  58 
 HIS   0.004   0.001   HIS A  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 6638)
  covalent geometry    : angle       0.58732 ( 9052)
  SS BOND              : bond        0.00256 (    4)
  SS BOND              : angle       0.95330 (    8)
  hydrogen bonds       : bond        0.05057 (  364)
  hydrogen bonds       : angle       4.83032 ( 1059)
  link_BETA1-4         : bond        0.00303 (    1)
  link_BETA1-4         : angle       1.87902 (    3)
  link_NAG-ASN         : bond        0.00289 (    1)
  link_NAG-ASN         : angle       1.15879 (    3)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 0.239 
Fit side-chains
TARDY: cannot create tardy model for: "CYS A 383 " (corrupted residue). Skipping it.
REVERT: A  129 TYR cc_start: 0.8356 (OUTLIER) cc_final: 0.8124 (m-80)
REVERT: A  391 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7218 (mm-30)
REVERT: L   26 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7724 (mt-10)
REVERT: L   32 CYS cc_start: 0.6956 (t) cc_final: 0.6490 (t)
REVERT: H   14 GLN cc_start: 0.8179 (pm20) cc_final: 0.7968 (pm20)
REVERT: H   90 GLN cc_start: 0.8265 (tt0) cc_final: 0.7542 (tp40)
REVERT: H  114 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.7517 (p0)
  outliers start: 19
  outliers final: 12
  residues processed: 115
  average time/residue: 0.0757
  time to fit residues: 11.7614
Evaluate side-chains
  106 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   60 TYR
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  129 TYR
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  383 CYS
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  423 MET
Chi-restraints excluded: chain A residue  609 HIS
Chi-restraints excluded: chain L residue   12 VAL
Chi-restraints excluded: chain L residue   14 THR
Chi-restraints excluded: chain L residue   43 THR
Chi-restraints excluded: chain L residue   93 VAL
Chi-restraints excluded: chain H residue  114 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 1 optimal weight:    5.9990
   chunk 28 optimal weight:    1.9990
   chunk 60 optimal weight:    0.5980
   chunk 52 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   chunk 66 optimal weight:    0.4980
   chunk 17 optimal weight:    2.9990
   chunk 63 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    1.1984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.148494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.102460 restraints weight = 7592.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.3104 rms_B_bonded: 2.36
r_work: 0.2954 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2796 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.3793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6644  Z= 0.173
  Angle     :  0.587   6.238   9066  Z= 0.302
  Chirality :  0.042   0.142   1028
  Planarity :  0.005   0.036   1115
  Dihedral  :  5.390  58.783    924
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 13.68 %
    Favored  : 83.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.27 (0.29), residues: 805
  helix:  1.38 (0.25), residues: 434
  sheet: -0.85 (0.45), residues: 127
  loop : -1.37 (0.37), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 240 
 TYR   0.020   0.002   TYR A 322 
 PHE   0.027   0.002   PHE A 546 
 TRP   0.011   0.001   TRP H  58 
 HIS   0.005   0.001   HIS A  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 6638)
  covalent geometry    : angle       0.58594 ( 9052)
  SS BOND              : bond        0.00394 (    4)
  SS BOND              : angle       0.99709 (    8)
  hydrogen bonds       : bond        0.05062 (  364)
  hydrogen bonds       : angle       4.66744 ( 1059)
  link_BETA1-4         : bond        0.00168 (    1)
  link_BETA1-4         : angle       1.72155 (    3)
  link_NAG-ASN         : bond        0.00253 (    1)
  link_NAG-ASN         : angle       1.15346 (    3)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.209 
Fit side-chains
TARDY: cannot create tardy model for: "CYS A 383 " (corrupted residue). Skipping it.
REVERT: A  129 TYR cc_start: 0.8352 (OUTLIER) cc_final: 0.8093 (m-80)
REVERT: A  195 TRP cc_start: 0.6609 (m-90) cc_final: 0.6106 (t60)
REVERT: A  391 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7232 (mm-30)
REVERT: A  572 LYS cc_start: 0.6114 (mtpp) cc_final: 0.5758 (mmtp)
REVERT: L   32 CYS cc_start: 0.6929 (t) cc_final: 0.6106 (t)
REVERT: L   69 ARG cc_start: 0.8551 (ttm110) cc_final: 0.8134 (ttp-110)
REVERT: H   48 ARG cc_start: 0.8086 (mtp85) cc_final: 0.7815 (mtp85)
REVERT: H   75 LYS cc_start: 0.8361 (tttp) cc_final: 0.8101 (tttp)
REVERT: H   79 THR cc_start: 0.8894 (m) cc_final: 0.8393 (p)
REVERT: H   90 GLN cc_start: 0.8336 (tt0) cc_final: 0.7383 (tp40)
REVERT: H  114 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.7427 (p0)
  outliers start: 17
  outliers final: 14
  residues processed: 110
  average time/residue: 0.0771
  time to fit residues: 11.6659
Evaluate side-chains
  114 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   60 TYR
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  129 TYR
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  383 CYS
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  423 MET
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain A residue  527 ASN
Chi-restraints excluded: chain A residue  609 HIS
Chi-restraints excluded: chain L residue   12 VAL
Chi-restraints excluded: chain L residue   14 THR
Chi-restraints excluded: chain L residue   43 THR
Chi-restraints excluded: chain H residue  114 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 59 optimal weight:    6.9990
   chunk 35 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 19 optimal weight:    5.9990
   chunk 80 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 38 optimal weight:    0.6980
   chunk 66 optimal weight:   10.0000
   chunk 55 optimal weight:    0.8980
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.150625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.105856 restraints weight = 7514.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.3043 rms_B_bonded: 2.30
r_work: 0.2895 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2741 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.4014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6644  Z= 0.132
  Angle     :  0.546   5.753   9066  Z= 0.279
  Chirality :  0.040   0.142   1028
  Planarity :  0.004   0.037   1115
  Dihedral  :  5.310  59.293    924
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 14.53 %
    Favored  : 83.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.53 (0.30), residues: 805
  helix:  1.50 (0.25), residues: 434
  sheet: -0.57 (0.46), residues: 128
  loop : -1.16 (0.39), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 240 
 TYR   0.015   0.001   TYR A 322 
 PHE   0.026   0.001   PHE A 546 
 TRP   0.012   0.001   TRP H  58 
 HIS   0.003   0.001   HIS A  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 6638)
  covalent geometry    : angle       0.54439 ( 9052)
  SS BOND              : bond        0.00264 (    4)
  SS BOND              : angle       0.90935 (    8)
  hydrogen bonds       : bond        0.04509 (  364)
  hydrogen bonds       : angle       4.45241 ( 1059)
  link_BETA1-4         : bond        0.00165 (    1)
  link_BETA1-4         : angle       1.68282 (    3)
  link_NAG-ASN         : bond        0.00328 (    1)
  link_NAG-ASN         : angle       1.11399 (    3)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 0.228 
Fit side-chains
TARDY: cannot create tardy model for: "CYS A 383 " (corrupted residue). Skipping it.
REVERT: A  129 TYR cc_start: 0.8305 (OUTLIER) cc_final: 0.8018 (m-80)
REVERT: A  195 TRP cc_start: 0.6616 (m-90) cc_final: 0.6092 (t60)
REVERT: A  391 GLU cc_start: 0.7509 (mt-10) cc_final: 0.6968 (mm-30)
REVERT: L   45 LYS cc_start: 0.7407 (mtpt) cc_final: 0.6913 (mtpt)
REVERT: L   69 ARG cc_start: 0.8559 (ttm110) cc_final: 0.8193 (ttp-110)
REVERT: H   48 ARG cc_start: 0.8066 (mtp85) cc_final: 0.7785 (mtp85)
REVERT: H   75 LYS cc_start: 0.8212 (tttp) cc_final: 0.7992 (tttp)
REVERT: H   79 THR cc_start: 0.8851 (m) cc_final: 0.8364 (p)
REVERT: H  114 ASP cc_start: 0.8539 (p0) cc_final: 0.7460 (p0)
  outliers start: 17
  outliers final: 15
  residues processed: 117
  average time/residue: 0.0761
  time to fit residues: 12.0848
Evaluate side-chains
  107 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   60 TYR
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  129 TYR
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  383 CYS
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  587 VAL
Chi-restraints excluded: chain L residue   12 VAL
Chi-restraints excluded: chain L residue   14 THR
Chi-restraints excluded: chain L residue   43 THR
Chi-restraints excluded: chain L residue   93 VAL
Chi-restraints excluded: chain L residue  116 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 14 optimal weight:    0.6980
   chunk 75 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 56 optimal weight:    0.3980
   chunk 27 optimal weight:    0.0670
   chunk 24 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
L  46 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.150917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.106096 restraints weight = 7498.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.3138 rms_B_bonded: 2.32
r_work: 0.2990 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2835 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.2835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.4216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6644  Z= 0.124
  Angle     :  0.540   5.537   9066  Z= 0.276
  Chirality :  0.039   0.127   1028
  Planarity :  0.004   0.038   1115
  Dihedral  :  5.189  58.823    924
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 15.94 %
    Favored  : 81.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (0.30), residues: 805
  helix:  1.66 (0.25), residues: 435
  sheet: -0.45 (0.45), residues: 127
  loop : -1.08 (0.39), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 240 
 TYR   0.014   0.001   TYR A  60 
 PHE   0.026   0.001   PHE A 546 
 TRP   0.012   0.001   TRP H  58 
 HIS   0.003   0.001   HIS A  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 6638)
  covalent geometry    : angle       0.53839 ( 9052)
  SS BOND              : bond        0.00169 (    4)
  SS BOND              : angle       1.24333 (    8)
  hydrogen bonds       : bond        0.04316 (  364)
  hydrogen bonds       : angle       4.32696 ( 1059)
  link_BETA1-4         : bond        0.00285 (    1)
  link_BETA1-4         : angle       1.61255 (    3)
  link_NAG-ASN         : bond        0.00332 (    1)
  link_NAG-ASN         : angle       1.12195 (    3)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.238 
Fit side-chains
TARDY: cannot create tardy model for: "CYS A 383 " (corrupted residue). Skipping it.
REVERT: A  129 TYR cc_start: 0.8322 (OUTLIER) cc_final: 0.8024 (m-80)
REVERT: A  195 TRP cc_start: 0.6674 (m-90) cc_final: 0.6014 (t60)
REVERT: A  391 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7199 (mm-30)
REVERT: A  572 LYS cc_start: 0.6041 (mtpt) cc_final: 0.5391 (mmtp)
REVERT: L   45 LYS cc_start: 0.7484 (mtpt) cc_final: 0.7284 (mtpt)
REVERT: L   69 ARG cc_start: 0.8558 (ttm110) cc_final: 0.8179 (ttp-110)
REVERT: H   48 ARG cc_start: 0.8042 (mtp85) cc_final: 0.7830 (mtp85)
REVERT: H   79 THR cc_start: 0.8906 (m) cc_final: 0.8483 (p)
REVERT: H  114 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.7573 (p0)
  outliers start: 18
  outliers final: 14
  residues processed: 111
  average time/residue: 0.0792
  time to fit residues: 11.8950
Evaluate side-chains
  114 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   60 TYR
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  129 TYR
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  383 CYS
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain A residue  527 ASN
Chi-restraints excluded: chain A residue  587 VAL
Chi-restraints excluded: chain A residue  609 HIS
Chi-restraints excluded: chain L residue   12 VAL
Chi-restraints excluded: chain L residue   14 THR
Chi-restraints excluded: chain L residue   43 THR
Chi-restraints excluded: chain H residue  114 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 70 optimal weight:    0.0020
   chunk 16 optimal weight:    7.9990
   chunk 2 optimal weight:    0.0670
   chunk 9 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 26 optimal weight:    0.2980
   chunk 47 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   overall best weight:    0.3726

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.152752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.108380 restraints weight = 7386.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.3172 rms_B_bonded: 2.29
r_work: 0.3024 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2870 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.4361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6644  Z= 0.109
  Angle     :  0.521   5.485   9066  Z= 0.264
  Chirality :  0.038   0.127   1028
  Planarity :  0.004   0.038   1115
  Dihedral  :  5.066  58.764    924
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 16.78 %
    Favored  : 81.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.90 (0.30), residues: 805
  helix:  1.80 (0.25), residues: 437
  sheet: -0.34 (0.45), residues: 128
  loop : -1.08 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 168 
 TYR   0.014   0.001   TYR A 567 
 PHE   0.026   0.001   PHE A 546 
 TRP   0.012   0.001   TRP H  58 
 HIS   0.002   0.001   HIS A  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 6638)
  covalent geometry    : angle       0.51892 ( 9052)
  SS BOND              : bond        0.00083 (    4)
  SS BOND              : angle       1.45585 (    8)
  hydrogen bonds       : bond        0.03974 (  364)
  hydrogen bonds       : angle       4.20372 ( 1059)
  link_BETA1-4         : bond        0.00220 (    1)
  link_BETA1-4         : angle       1.53525 (    3)
  link_NAG-ASN         : bond        0.00337 (    1)
  link_NAG-ASN         : angle       1.09933 (    3)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.234 
Fit side-chains
TARDY: cannot create tardy model for: "CYS A 383 " (corrupted residue). Skipping it.
REVERT: A  129 TYR cc_start: 0.8292 (OUTLIER) cc_final: 0.7982 (m-80)
REVERT: A  194 GLN cc_start: 0.8191 (mm-40) cc_final: 0.7871 (mm-40)
REVERT: A  195 TRP cc_start: 0.6669 (m-90) cc_final: 0.6047 (t60)
REVERT: A  391 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7175 (mm-30)
REVERT: A  410 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8116 (tpp)
REVERT: A  572 LYS cc_start: 0.6047 (mtpt) cc_final: 0.5401 (mmtt)
REVERT: L   69 ARG cc_start: 0.8512 (ttm110) cc_final: 0.8135 (ttp-110)
REVERT: L   87 THR cc_start: 0.8069 (m) cc_final: 0.7751 (t)
REVERT: H   75 LYS cc_start: 0.8274 (tttp) cc_final: 0.7998 (tttp)
REVERT: H   79 THR cc_start: 0.8882 (m) cc_final: 0.8495 (p)
REVERT: H  114 ASP cc_start: 0.8562 (p0) cc_final: 0.7713 (p0)
  outliers start: 15
  outliers final: 11
  residues processed: 113
  average time/residue: 0.0728
  time to fit residues: 11.2799
Evaluate side-chains
  109 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   60 TYR
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  129 TYR
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  383 CYS
Chi-restraints excluded: chain A residue  410 MET
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  587 VAL
Chi-restraints excluded: chain L residue   12 VAL
Chi-restraints excluded: chain L residue   14 THR
Chi-restraints excluded: chain L residue   21 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 19 optimal weight:    4.9990
   chunk 25 optimal weight:    0.5980
   chunk 58 optimal weight:    0.3980
   chunk 18 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 1 optimal weight:    7.9990
   chunk 34 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.9582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.150061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.105272 restraints weight = 7471.834|
|-----------------------------------------------------------------------------|
r_work (start): 0.3128 rms_B_bonded: 2.29
r_work: 0.2978 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2825 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.4392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6644  Z= 0.148
  Angle     :  0.554   5.734   9066  Z= 0.282
  Chirality :  0.040   0.126   1028
  Planarity :  0.004   0.039   1115
  Dihedral  :  5.098  57.125    924
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 16.78 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.30), residues: 805
  helix:  1.75 (0.25), residues: 436
  sheet: -0.25 (0.45), residues: 128
  loop : -1.10 (0.39), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 240 
 TYR   0.016   0.001   TYR A 567 
 PHE   0.029   0.001   PHE A 546 
 TRP   0.013   0.001   TRP H  58 
 HIS   0.004   0.001   HIS A  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 6638)
  covalent geometry    : angle       0.55025 ( 9052)
  SS BOND              : bond        0.00272 (    4)
  SS BOND              : angle       1.94466 (    8)
  hydrogen bonds       : bond        0.04474 (  364)
  hydrogen bonds       : angle       4.28024 ( 1059)
  link_BETA1-4         : bond        0.00100 (    1)
  link_BETA1-4         : angle       1.53230 (    3)
  link_NAG-ASN         : bond        0.00277 (    1)
  link_NAG-ASN         : angle       1.12126 (    3)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 97
  time to evaluate  : 0.246 
Fit side-chains
TARDY: cannot create tardy model for: "CYS A 383 " (corrupted residue). Skipping it.
REVERT: A  129 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.8005 (m-80)
REVERT: A  195 TRP cc_start: 0.6770 (m-90) cc_final: 0.6131 (t60)
REVERT: A  197 MET cc_start: 0.7888 (mmp) cc_final: 0.7655 (mmp)
REVERT: A  391 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7335 (mm-30)
REVERT: A  410 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8237 (tpp)
REVERT: A  572 LYS cc_start: 0.6072 (mtpt) cc_final: 0.5434 (mmtt)
REVERT: L   69 ARG cc_start: 0.8522 (ttm110) cc_final: 0.8247 (ttp-110)
REVERT: L   97 ASP cc_start: 0.7394 (m-30) cc_final: 0.7078 (m-30)
REVERT: H   75 LYS cc_start: 0.8216 (tttp) cc_final: 0.7938 (tttp)
REVERT: H   79 THR cc_start: 0.8893 (m) cc_final: 0.8513 (p)
REVERT: H  114 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.7829 (p0)
  outliers start: 21
  outliers final: 15
  residues processed: 110
  average time/residue: 0.0765
  time to fit residues: 11.4315
Evaluate side-chains
  111 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   60 TYR
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  129 TYR
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  383 CYS
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  410 MET
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  527 ASN
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  587 VAL
Chi-restraints excluded: chain L residue   12 VAL
Chi-restraints excluded: chain L residue   14 THR
Chi-restraints excluded: chain L residue   21 VAL
Chi-restraints excluded: chain L residue  116 THR
Chi-restraints excluded: chain H residue  114 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 70 optimal weight:    9.9990
   chunk 65 optimal weight:    3.9990
   chunk 20 optimal weight:    0.6980
   chunk 60 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 17 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 43 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    1.5184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.146810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.100420 restraints weight = 7673.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.3075 rms_B_bonded: 2.37
r_work: 0.2928 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2774 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.4417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   6644  Z= 0.198
  Angle     :  0.601   6.202   9066  Z= 0.309
  Chirality :  0.042   0.131   1028
  Planarity :  0.005   0.039   1115
  Dihedral  :  5.412  56.388    924
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 16.78 %
    Favored  : 79.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.30), residues: 805
  helix:  1.56 (0.25), residues: 435
  sheet: -0.30 (0.45), residues: 127
  loop : -1.15 (0.39), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 240 
 TYR   0.020   0.002   TYR A 322 
 PHE   0.032   0.002   PHE A 546 
 TRP   0.013   0.001   TRP H  58 
 HIS   0.004   0.001   HIS A  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 ( 6638)
  covalent geometry    : angle       0.59701 ( 9052)
  SS BOND              : bond        0.00250 (    4)
  SS BOND              : angle       2.01330 (    8)
  hydrogen bonds       : bond        0.05096 (  364)
  hydrogen bonds       : angle       4.48336 ( 1059)
  link_BETA1-4         : bond        0.00165 (    1)
  link_BETA1-4         : angle       1.68054 (    3)
  link_NAG-ASN         : bond        0.00242 (    1)
  link_NAG-ASN         : angle       1.30085 (    3)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 99
  time to evaluate  : 0.232 
Fit side-chains
TARDY: cannot create tardy model for: "CYS A 383 " (corrupted residue). Skipping it.
REVERT: A  129 TYR cc_start: 0.8438 (OUTLIER) cc_final: 0.7991 (m-10)
REVERT: A  195 TRP cc_start: 0.6789 (m-90) cc_final: 0.6115 (t60)
REVERT: A  391 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7407 (mm-30)
REVERT: A  410 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8381 (tpp)
REVERT: A  502 MET cc_start: 0.8313 (ttm) cc_final: 0.8063 (mtt)
REVERT: A  572 LYS cc_start: 0.6128 (mtpt) cc_final: 0.5397 (mmtp)
REVERT: L   30 MET cc_start: 0.6651 (mmt) cc_final: 0.6443 (mmt)
REVERT: L   69 ARG cc_start: 0.8561 (ttm110) cc_final: 0.8301 (ttp-110)
REVERT: L   97 ASP cc_start: 0.7434 (m-30) cc_final: 0.7093 (m-30)
REVERT: H   75 LYS cc_start: 0.8227 (tttp) cc_final: 0.7961 (tttp)
REVERT: H   79 THR cc_start: 0.8921 (m) cc_final: 0.8531 (p)
REVERT: H  114 ASP cc_start: 0.8651 (OUTLIER) cc_final: 0.7998 (p0)
  outliers start: 23
  outliers final: 17
  residues processed: 112
  average time/residue: 0.0763
  time to fit residues: 11.5999
Evaluate side-chains
  114 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   60 TYR
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  129 TYR
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  383 CYS
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  410 MET
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain A residue  527 ASN
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  587 VAL
Chi-restraints excluded: chain A residue  609 HIS
Chi-restraints excluded: chain L residue   12 VAL
Chi-restraints excluded: chain L residue   14 THR
Chi-restraints excluded: chain L residue  116 THR
Chi-restraints excluded: chain H residue  114 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 29 optimal weight:    0.5980
   chunk 35 optimal weight:    4.9990
   chunk 79 optimal weight:    0.5980
   chunk 1 optimal weight:    5.9990
   chunk 39 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 68 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0470
   overall best weight:    0.5278

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.150568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.105723 restraints weight = 7410.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.3130 rms_B_bonded: 2.30
r_work: 0.2981 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2826 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.4534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6644  Z= 0.121
  Angle     :  0.541   6.644   9066  Z= 0.275
  Chirality :  0.039   0.138   1028
  Planarity :  0.004   0.038   1115
  Dihedral  :  5.189  57.761    924
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 17.63 %
    Favored  : 79.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.84 (0.30), residues: 805
  helix:  1.70 (0.25), residues: 436
  sheet: -0.21 (0.45), residues: 128
  loop : -1.09 (0.39), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 240 
 TYR   0.015   0.001   TYR L  64 
 PHE   0.028   0.001   PHE A 546 
 TRP   0.013   0.001   TRP A 205 
 HIS   0.003   0.001   HIS A  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 6638)
  covalent geometry    : angle       0.53814 ( 9052)
  SS BOND              : bond        0.00140 (    4)
  SS BOND              : angle       1.57522 (    8)
  hydrogen bonds       : bond        0.04272 (  364)
  hydrogen bonds       : angle       4.26307 ( 1059)
  link_BETA1-4         : bond        0.00332 (    1)
  link_BETA1-4         : angle       1.63250 (    3)
  link_NAG-ASN         : bond        0.00283 (    1)
  link_NAG-ASN         : angle       1.30389 (    3)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.179 
Fit side-chains
TARDY: cannot create tardy model for: "CYS A 383 " (corrupted residue). Skipping it.
REVERT: A  129 TYR cc_start: 0.8325 (OUTLIER) cc_final: 0.8050 (m-80)
REVERT: A  195 TRP cc_start: 0.6714 (m-90) cc_final: 0.6013 (t60)
REVERT: A  391 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7299 (mm-30)
REVERT: A  410 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8218 (tpp)
REVERT: A  502 MET cc_start: 0.8280 (ttm) cc_final: 0.8035 (mtt)
REVERT: A  572 LYS cc_start: 0.6160 (mtpt) cc_final: 0.5431 (mmtp)
REVERT: L   69 ARG cc_start: 0.8530 (ttm110) cc_final: 0.8266 (ttp-110)
REVERT: L   87 THR cc_start: 0.8037 (m) cc_final: 0.7660 (t)
REVERT: L   97 ASP cc_start: 0.7338 (m-30) cc_final: 0.7086 (m-30)
REVERT: H   75 LYS cc_start: 0.8173 (tttp) cc_final: 0.7898 (tttp)
REVERT: H   79 THR cc_start: 0.8880 (m) cc_final: 0.8493 (p)
REVERT: H  114 ASP cc_start: 0.8576 (OUTLIER) cc_final: 0.7876 (p0)
  outliers start: 17
  outliers final: 14
  residues processed: 109
  average time/residue: 0.0697
  time to fit residues: 10.4896
Evaluate side-chains
  111 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   60 TYR
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  129 TYR
Chi-restraints excluded: chain A residue  336 CYS
Chi-restraints excluded: chain A residue  383 CYS
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  410 MET
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  527 ASN
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  587 VAL
Chi-restraints excluded: chain L residue   12 VAL
Chi-restraints excluded: chain L residue   14 THR
Chi-restraints excluded: chain L residue  116 THR
Chi-restraints excluded: chain H residue  114 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 39 optimal weight:    0.5980
   chunk 74 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0980
   chunk 51 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.149803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.104437 restraints weight = 7468.034|
|-----------------------------------------------------------------------------|
r_work (start): 0.3131 rms_B_bonded: 2.34
r_work: 0.2985 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2829 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.4577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6644  Z= 0.125
  Angle     :  0.542   7.798   9066  Z= 0.275
  Chirality :  0.039   0.132   1028
  Planarity :  0.004   0.038   1115
  Dihedral  :  5.135  57.061    924
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 17.77 %
    Favored  : 79.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.30), residues: 805
  helix:  1.73 (0.25), residues: 436
  sheet: -0.19 (0.46), residues: 128
  loop : -1.11 (0.39), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 240 
 TYR   0.015   0.001   TYR L  64 
 PHE   0.029   0.001   PHE A 546 
 TRP   0.013   0.001   TRP H  58 
 HIS   0.003   0.001   HIS A  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 6638)
  covalent geometry    : angle       0.53931 ( 9052)
  SS BOND              : bond        0.00253 (    4)
  SS BOND              : angle       1.47814 (    8)
  hydrogen bonds       : bond        0.04284 (  364)
  hydrogen bonds       : angle       4.26506 ( 1059)
  link_BETA1-4         : bond        0.00164 (    1)
  link_BETA1-4         : angle       1.54108 (    3)
  link_NAG-ASN         : bond        0.00284 (    1)
  link_NAG-ASN         : angle       1.23657 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1951.29 seconds
wall clock time: 33 minutes 59.19 seconds (2039.19 seconds total)