Starting phenix.real_space_refine
on Fri Aug 22 18:04:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7li6_23361/08_2025/7li6_23361.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7li6_23361/08_2025/7li6_23361.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7li6_23361/08_2025/7li6_23361.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7li6_23361/08_2025/7li6_23361.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7li6_23361/08_2025/7li6_23361.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7li6_23361/08_2025/7li6_23361.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.040
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: 5
    Type Number    sf(0)   Gaussians
     S      34      5.16       5
     Cl      1      4.86       5
     C    4178      2.51       5
     N     958      2.21       5
     O    1078      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6249
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4284
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 539, 4284
          Classifications: {'peptide': 539}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 23, 'TRANS': 515}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "B"
      Number of atoms: 912
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 912
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 3, 'TRANS': 114}
    Chain: "C"
      Number of atoms: 829
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 829
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 6, 'TRANS': 103}
    Chain: "D"
      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
    Chain: "A"
      Number of atoms: 196
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 196
          Unusual residues: {' CL': 1, 'D10': 6, 'D12': 3, 'HP6': 9, 'LNK': 4, 'R16': 1}
          Classifications: {'undetermined': 24}
          Link IDs: {None: 23}
  Time building chain proxies: 1.47, per 1000 atoms: 0.24
  Number of scatterers: 6249
  At special positions: 0
  Unit cell: (70.066, 79.981, 123.607, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      1     17.00
     S      34     16.00
     O    1078      8.00
     N     958      7.00
     C    4178      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 200 " - pdb=" SG  CYS A 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  41 " - pdb=" SG  CYS B 115 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  43 " - pdb=" SG  CYS C 112 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Links applied
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG D   1 " - " ASN A 208 "
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.60
  Conformation dependent library (CDL) restraints added in 284.3 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1400

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 7 sheets defined
      51.5% alpha, 8.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 82 through 87
    Processing helix  chain 'A' and resid 88 through 93
    Processing helix  chain 'A' and resid 103 through 112
      removed outlier: 3.597A  pdb=" N   TYR A 107 " --> pdb=" O   TRP A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 129
    Processing helix  chain 'A' and resid 129 through 143
    Processing helix  chain 'A' and resid 149 through 153
    Processing helix  chain 'A' and resid 159 through 190
      removed outlier: 4.332A  pdb=" N   TYR A 163 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   ASN A 177 " --> pdb=" O   ALA A 173 " (cutoff:3.500A)
      removed outlier: 5.112A  pdb=" N   THR A 178 " --> pdb=" O   SER A 174 " (cutoff:3.500A)
      removed outlier: 4.814A  pdb=" N   ILE A 179 " --> pdb=" O   TYR A 175 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   MET A 180 " --> pdb=" O   TYR A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 235
    Processing helix  chain 'A' and resid 252 through 268
      removed outlier: 4.324A  pdb=" N   CYS A 258 " --> pdb=" O   GLN A 254 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   LEU A 261 " --> pdb=" O   LEU A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 285
    Processing helix  chain 'A' and resid 285 through 301
      removed outlier: 4.174A  pdb=" N   TYR A 289 " --> pdb=" O   ALA A 285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 313
      removed outlier: 3.528A  pdb=" N   VAL A 309 " --> pdb=" O   ALA A 305 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LEU A 310 " --> pdb=" O   TRP A 306 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   PHE A 311 " --> pdb=" O   ARG A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 322
      removed outlier: 3.763A  pdb=" N   LEU A 321 " --> pdb=" O   TRP A 317 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   GLU A 322 " --> pdb=" O   GLN A 318 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 317 through 322'
    Processing helix  chain 'A' and resid 325 through 338
      removed outlier: 3.909A  pdb=" N   GLY A 338 " --> pdb=" O   PHE A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 348
      removed outlier: 3.518A  pdb=" N   ALA A 346 " --> pdb=" O   GLY A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 391
    Processing helix  chain 'A' and resid 393 through 397
      removed outlier: 3.800A  pdb=" N   VAL A 397 " --> pdb=" O   VAL A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 415
      removed outlier: 4.248A  pdb=" N   ALA A 411 " --> pdb=" O   PHE A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 443
      removed outlier: 4.000A  pdb=" N   ALA A 441 " --> pdb=" O   ASP A 437 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   GLY A 442 " --> pdb=" O   SER A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 454
      removed outlier: 3.813A  pdb=" N   ILE A 447 " --> pdb=" O   LEU A 443 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   ALA A 449 " --> pdb=" O   GLY A 445 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ASP A 452 " --> pdb=" O   THR A 448 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   GLU A 453 " --> pdb=" O   ALA A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 462
      removed outlier: 4.454A  pdb=" N   ARG A 461 " --> pdb=" O   VAL A 457 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ARG A 462 " --> pdb=" O   TRP A 458 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 457 through 462'
    Processing helix  chain 'A' and resid 463 through 476
      removed outlier: 3.521A  pdb=" N   ALA A 468 " --> pdb=" O   ARG A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 490
      removed outlier: 3.659A  pdb=" N   LYS A 490 " --> pdb=" O   ALA A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 490 through 495
      removed outlier: 4.402A  pdb=" N   GLU A 494 " --> pdb=" O   LYS A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 515
    Processing helix  chain 'A' and resid 517 through 530
    Processing helix  chain 'A' and resid 534 through 544
      removed outlier: 4.105A  pdb=" N   TRP A 541 " --> pdb=" O   TRP A 537 " (cutoff:3.500A)
      removed outlier: 4.848A  pdb=" N   VAL A 542 " --> pdb=" O   ARG A 538 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ALA A 543 " --> pdb=" O   ILE A 539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 559
    Processing helix  chain 'A' and resid 572 through 585
      removed outlier: 4.354A  pdb=" N   ILE A 576 " --> pdb=" O   TYR A 572 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   SER A 585 " --> pdb=" O   ILE A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 600
      removed outlier: 3.656A  pdb=" N   LEU A 597 " --> pdb=" O   ILE A 593 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   ILE A 598 " --> pdb=" O   ALA A 594 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   ILE A 599 " --> pdb=" O   TYR A 595 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   THR A 600 " --> pdb=" O   ARG A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 613
      removed outlier: 3.634A  pdb=" N   THR A 613 " --> pdb=" O   ILE A 609 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 51
      removed outlier: 3.987A  pdb=" N   TYR B  50 " --> pdb=" O   ARG B  47 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   SER B  51 " --> pdb=" O   PHE B  48 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 47 through 51'
    Processing sheet with id=AA1, first strand: chain 'B' and resid 22 through 25
      removed outlier: 3.827A  pdb=" N   VAL B  37 " --> pdb=" O   LEU B 102 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 77 through 79
      removed outlier: 7.174A  pdb=" N   TRP B  55 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
      removed outlier: 4.875A  pdb=" N   ARG B  69 " --> pdb=" O   MET B  53 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   MET B  53 " --> pdb=" O   ARG B  69 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 77 through 79
      removed outlier: 7.174A  pdb=" N   TRP B  55 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
      removed outlier: 4.875A  pdb=" N   ARG B  69 " --> pdb=" O   MET B  53 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   MET B  53 " --> pdb=" O   ARG B  69 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   TYR B 113 " --> pdb=" O   THR B 134 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 25 through 26
      removed outlier: 3.567A  pdb=" N   THR C  25 " --> pdb=" O   ARG C  44 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 30 through 31
      removed outlier: 3.731A  pdb=" N   LEU C  31 " --> pdb=" O   LYS C 127 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   THR C 126 " --> pdb=" O   TYR C 110 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   TYR C 110 " --> pdb=" O   THR C 126 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'C' and resid 77 through 78
      removed outlier: 3.538A  pdb=" N   TYR C  73 " --> pdb=" O   ASN C  77 " (cutoff:3.500A)
      removed outlier: 5.209A  pdb=" N   LEU C  70 " --> pdb=" O   GLN C  61 " (cutoff:3.500A)
      removed outlier: 5.851A  pdb=" N   GLN C  61 " --> pdb=" O   LEU C  70 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 87 through 89

    265 hydrogen bonds defined for protein.
    765 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.82

  Time building geometry restraints manager: 0.79 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1808
        1.34 -     1.46: 1610
        1.46 -     1.58: 2936
        1.58 -     1.69: 0
        1.69 -     1.81: 49
  Bond restraints: 6403
  Sorted by residual:
  bond pdb=" C1  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.25e+00
  bond pdb=" C2  NAG D   1 "
       pdb=" N2  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.439  1.464 -0.025 2.00e-02 2.50e+03 1.52e+00
  bond pdb=" C1  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.431 -0.025 2.00e-02 2.50e+03 1.51e+00
  bond pdb=" C5  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.436 -0.023 2.00e-02 2.50e+03 1.30e+00
  bond pdb=" C5  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.25e+00
  ... (remaining 6398 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.11: 8224
        1.11 -     2.22: 194
        2.22 -     3.34: 91
        3.34 -     4.45: 111
        4.45 -     5.56: 12
  Bond angle restraints: 8632
  Sorted by residual:
  angle pdb=" N   TYR A 495 "
        pdb=" CA  TYR A 495 "
        pdb=" C   TYR A 495 "
      ideal   model   delta    sigma   weight residual
     114.04  110.66    3.38 1.24e+00 6.50e-01 7.43e+00
  angle pdb=" N   VAL A 102 "
        pdb=" CA  VAL A 102 "
        pdb=" C   VAL A 102 "
      ideal   model   delta    sigma   weight residual
     113.39  109.50    3.89 1.47e+00 4.63e-01 7.01e+00
  angle pdb=" C   ALA C  74 "
        pdb=" N   ALA C  75 "
        pdb=" CA  ALA C  75 "
      ideal   model   delta    sigma   weight residual
     121.54  126.36   -4.82 1.91e+00 2.74e-01 6.38e+00
  angle pdb=" CA  GLY C  90 "
        pdb=" C   GLY C  90 "
        pdb=" O   GLY C  90 "
      ideal   model   delta    sigma   weight residual
     122.22  120.64    1.58 6.50e-01 2.37e+00 5.92e+00
  angle pdb=" C   ARG A 461 "
        pdb=" N   ARG A 462 "
        pdb=" CA  ARG A 462 "
      ideal   model   delta    sigma   weight residual
     121.54  126.02   -4.48 1.91e+00 2.74e-01 5.51e+00
  ... (remaining 8627 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.66: 3426
       17.66 -    35.32: 225
       35.32 -    52.98: 48
       52.98 -    70.64: 6
       70.64 -    88.30: 6
  Dihedral angle restraints: 3711
    sinusoidal: 1505
      harmonic: 2206
  Sorted by residual:
  dihedral pdb=" CB  CYS A 200 "
           pdb=" SG  CYS A 200 "
           pdb=" SG  CYS A 209 "
           pdb=" CB  CYS A 209 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -150.26   64.26     1      1.00e+01 1.00e-02 5.43e+01
  dihedral pdb=" CB  GLU A 606 "
           pdb=" CG  GLU A 606 "
           pdb=" CD  GLU A 606 "
           pdb=" OE1 GLU A 606 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.30  -88.30     1      3.00e+01 1.11e-03 1.03e+01
  dihedral pdb=" CB  GLU A 412 "
           pdb=" CG  GLU A 412 "
           pdb=" CD  GLU A 412 "
           pdb=" OE1 GLU A 412 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   83.56  -83.56     1      3.00e+01 1.11e-03 9.47e+00
  ... (remaining 3708 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.331: 941
       0.331 -    0.661: 0
       0.661 -    0.992: 0
       0.992 -    1.322: 0
       1.322 -    1.653: 1
  Chirality restraints: 942
  Sorted by residual:
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -0.75   -1.65 2.00e-02 2.50e+03 6.83e+03
  chirality pdb=" C2  NAG D   1 "
            pdb=" C1  NAG D   1 "
            pdb=" C3  NAG D   1 "
            pdb=" N2  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.32   -0.17 2.00e-01 2.50e+01 7.43e-01
  chirality pdb=" CB  ILE C  99 "
            pdb=" CA  ILE C  99 "
            pdb=" CG1 ILE C  99 "
            pdb=" CG2 ILE C  99 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.79   -0.14 2.00e-01 2.50e+01 5.00e-01
  ... (remaining 939 not shown)

  Planarity restraints: 1045
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 338 "   -0.026 5.00e-02 4.00e+02   3.93e-02 2.47e+00
        pdb=" N   PRO A 339 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 339 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 339 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 287 "   -0.023 5.00e-02 4.00e+02   3.51e-02 1.97e+00
        pdb=" N   PRO A 288 "    0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO A 288 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 288 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A  88 "   -0.006 2.00e-02 2.50e+03   1.14e-02 1.30e+00
        pdb=" C   PHE A  88 "    0.020 2.00e-02 2.50e+03
        pdb=" O   PHE A  88 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   LEU A  89 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 1042 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 1963
        2.83 -     3.35: 5435
        3.35 -     3.86: 9805
        3.86 -     4.38: 10688
        4.38 -     4.90: 19047
  Nonbonded interactions: 46938
  Sorted by model distance:
  nonbonded pdb=" O   SER A 190 "
            pdb=" OG  SER A 190 "
     model   vdw
     2.310 3.040
  nonbonded pdb=" O   GLU A 229 "
            pdb=" OG1 THR A 233 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" NE2 GLN C 114 "
            pdb=" O   SER C 119 "
     model   vdw
     2.312 3.120
  nonbonded pdb=" O   VAL A 297 "
            pdb=" OG1 THR A 301 "
     model   vdw
     2.328 3.040
  nonbonded pdb=" OG  SER C  87 "
            pdb=" OD1 ASN C  98 "
     model   vdw
     2.354 3.040
  ... (remaining 46933 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.910
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.630
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7005
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      :  0.002   0.065   6409  Z= 0.111
  Angle     :  0.744  28.058   8644  Z= 0.324
  Chirality :  0.066   1.653    942
  Planarity :  0.003   0.039   1044
  Dihedral  : 12.312  88.297   2302
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  :  9.53 %
    Favored  : 88.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.07 (0.27), residues: 761
  helix: -0.87 (0.25), residues: 343
  sheet: -2.44 (0.62), residues: 76
  loop : -3.22 (0.28), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 234 
 TYR   0.011   0.001   TYR A 175 
 PHE   0.003   0.000   PHE A  88 
 TRP   0.004   0.000   TRP A 282 
 HIS   0.001   0.000   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00192 ( 6403)
  covalent geometry    : angle       0.66671 ( 8632)
  SS BOND              : bond        0.00070 (    3)
  SS BOND              : angle       0.21395 (    6)
  hydrogen bonds       : bond        0.19283 (  260)
  hydrogen bonds       : angle       5.83562 (  765)
  Misc. bond           : bond        0.00064 (    1)
  link_BETA1-4         : bond        0.06474 (    1)
  link_BETA1-4         : angle      17.65278 (    3)
  link_NAG-ASN         : bond        0.00286 (    1)
  link_NAG-ASN         : angle       1.79528 (    3)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.176 
Fit side-chains
REVERT: A  306 TRP cc_start: 0.7018 (t-100) cc_final: 0.6154 (p-90)
REVERT: A  514 TRP cc_start: 0.7063 (m-10) cc_final: 0.6686 (m100)
REVERT: A  535 TRP cc_start: 0.6493 (t60) cc_final: 0.6135 (p-90)
REVERT: A  607 ARG cc_start: 0.7332 (mtt180) cc_final: 0.7032 (mtt180)
REVERT: B   99 TYR cc_start: 0.8296 (m-80) cc_final: 0.8051 (m-80)
REVERT: C   69 LYS cc_start: 0.7459 (tttp) cc_final: 0.7254 (tttm)
REVERT: C   71 LEU cc_start: 0.7884 (tp) cc_final: 0.7629 (tp)
REVERT: C  116 LYS cc_start: 0.6969 (tttt) cc_final: 0.6637 (mttp)
  outliers start: 11
  outliers final: 7
  residues processed: 110
  average time/residue: 0.1084
  time to fit residues: 14.6381
Evaluate side-chains
  73 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain C residue   82 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.2980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
A 111 GLN
A 145 ASN
A 254 GLN
A 318 GLN
A 416 ASN
A 520 GLN
B  24 GLN
C  98 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.166176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.144384 restraints weight = 7182.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.144478 restraints weight = 6168.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.146031 restraints weight = 5922.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.146908 restraints weight = 4695.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.147572 restraints weight = 4127.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.2645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   6409  Z= 0.210
  Angle     :  0.646  10.587   8644  Z= 0.331
  Chirality :  0.044   0.226    942
  Planarity :  0.004   0.034   1044
  Dihedral  :  6.056  58.650   1009
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.96 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 15.16 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.14 (0.30), residues: 761
  helix: -0.01 (0.28), residues: 349
  sheet: -2.08 (0.57), residues: 95
  loop : -2.87 (0.31), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  85 
 TYR   0.023   0.002   TYR A 176 
 PHE   0.022   0.002   PHE A 213 
 TRP   0.017   0.002   TRP A 204 
 HIS   0.002   0.001   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00502 ( 6403)
  covalent geometry    : angle       0.64384 ( 8632)
  SS BOND              : bond        0.00299 (    3)
  SS BOND              : angle       1.39129 (    6)
  hydrogen bonds       : bond        0.04583 (  260)
  hydrogen bonds       : angle       4.33583 (  765)
  Misc. bond           : bond        0.00076 (    1)
  link_BETA1-4         : bond        0.00117 (    1)
  link_BETA1-4         : angle       0.82565 (    3)
  link_NAG-ASN         : bond        0.00422 (    1)
  link_NAG-ASN         : angle       2.16385 (    3)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 83
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
REVERT: A  306 TRP cc_start: 0.7198 (t-100) cc_final: 0.6755 (p-90)
REVERT: A  370 MET cc_start: 0.7344 (mmp) cc_final: 0.7106 (mmt)
REVERT: B   53 MET cc_start: 0.8271 (mmt) cc_final: 0.7988 (mmt)
REVERT: C  116 LYS cc_start: 0.7765 (tttt) cc_final: 0.7097 (mtmt)
  outliers start: 24
  outliers final: 17
  residues processed: 100
  average time/residue: 0.0814
  time to fit residues: 10.6880
Evaluate side-chains
  82 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 65
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  126 ILE
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  209 CYS
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  396 GLU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue  107 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 72 optimal weight:    0.4980
   chunk 35 optimal weight:    0.5980
   chunk 0 optimal weight:   30.0000
   chunk 39 optimal weight:    0.8980
   chunk 57 optimal weight:    0.5980
   chunk 27 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 111 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.158105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.122545 restraints weight = 7531.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.128028 restraints weight = 4415.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.131649 restraints weight = 3143.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.133876 restraints weight = 2508.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.135753 restraints weight = 2159.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6930
moved from start:          0.2911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6409  Z= 0.130
  Angle     :  0.551   9.557   8644  Z= 0.279
  Chirality :  0.041   0.260    942
  Planarity :  0.004   0.032   1044
  Dihedral  :  5.613  56.748   1007
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.83 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 16.88 %
    Favored  : 78.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.65 (0.31), residues: 761
  helix:  0.41 (0.28), residues: 353
  sheet: -1.54 (0.59), residues: 89
  loop : -2.76 (0.31), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  38 
 TYR   0.024   0.002   TYR A 176 
 PHE   0.013   0.001   PHE A 380 
 TRP   0.008   0.001   TRP B  66 
 HIS   0.001   0.001   HIS A 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 6403)
  covalent geometry    : angle       0.54797 ( 8632)
  SS BOND              : bond        0.00238 (    3)
  SS BOND              : angle       1.38589 (    6)
  hydrogen bonds       : bond        0.03796 (  260)
  hydrogen bonds       : angle       4.15641 (  765)
  Misc. bond           : bond        0.00024 (    1)
  link_BETA1-4         : bond        0.00581 (    1)
  link_BETA1-4         : angle       1.24016 (    3)
  link_NAG-ASN         : bond        0.00033 (    1)
  link_NAG-ASN         : angle       2.10076 (    3)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 68
  time to evaluate  : 0.191 
Fit side-chains
REVERT: A  306 TRP cc_start: 0.6927 (t-100) cc_final: 0.5673 (p-90)
REVERT: A  385 TYR cc_start: 0.6592 (OUTLIER) cc_final: 0.6236 (t80)
REVERT: A  386 MET cc_start: 0.6911 (ttp) cc_final: 0.6705 (mtm)
REVERT: A  564 ARG cc_start: 0.8243 (ttt90) cc_final: 0.7742 (ttt90)
REVERT: C  116 LYS cc_start: 0.7696 (tttt) cc_final: 0.6396 (mtmt)
  outliers start: 28
  outliers final: 19
  residues processed: 88
  average time/residue: 0.0867
  time to fit residues: 9.9782
Evaluate side-chains
  83 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 63
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  126 ILE
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  197 TRP
Chi-restraints excluded: chain A residue  209 CYS
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  385 TYR
Chi-restraints excluded: chain A residue  396 GLU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain B residue   70 ILE
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue  107 THR
Chi-restraints excluded: chain C residue  118 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 47 optimal weight:    0.9990
   chunk 72 optimal weight:    7.9990
   chunk 13 optimal weight:    3.9990
   chunk 2 optimal weight:    0.8980
   chunk 49 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 34 optimal weight:    0.5980
   chunk 32 optimal weight:    0.0970
   chunk 41 optimal weight:    0.4980
   chunk 65 optimal weight:    0.0060
   overall best weight:    0.3794

-------------------------------------------------------------------------------
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 = 0.3832 r_free = 0.3832 target = 0.159480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.124283 restraints weight = 7411.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.129833 restraints weight = 4297.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.133561 restraints weight = 3017.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.136073 restraints weight = 2380.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.137834 restraints weight = 2023.421|
|-----------------------------------------------------------------------------|
r_work (final): 0.3602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6854
moved from start:          0.3020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6409  Z= 0.101
  Angle     :  0.514   9.494   8644  Z= 0.259
  Chirality :  0.040   0.260    942
  Planarity :  0.004   0.030   1044
  Dihedral  :  5.061  57.037   1004
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 17.66 %
    Favored  : 77.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.32 (0.31), residues: 761
  helix:  0.62 (0.29), residues: 354
  sheet: -1.24 (0.60), residues: 92
  loop : -2.57 (0.33), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  38 
 TYR   0.022   0.001   TYR A 176 
 PHE   0.012   0.001   PHE A 133 
 TRP   0.011   0.001   TRP A 197 
 HIS   0.001   0.000   HIS C 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 6403)
  covalent geometry    : angle       0.50977 ( 8632)
  SS BOND              : bond        0.00173 (    3)
  SS BOND              : angle       1.84480 (    6)
  hydrogen bonds       : bond        0.03198 (  260)
  hydrogen bonds       : angle       4.03758 (  765)
  Misc. bond           : bond        0.00016 (    1)
  link_BETA1-4         : bond        0.00571 (    1)
  link_BETA1-4         : angle       0.84492 (    3)
  link_NAG-ASN         : bond        0.00224 (    1)
  link_NAG-ASN         : angle       2.21238 (    3)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 66
  time to evaluate  : 0.193 
Fit side-chains
REVERT: A  247 ASP cc_start: 0.8369 (t0) cc_final: 0.8083 (t0)
REVERT: A  347 PHE cc_start: 0.6891 (m-80) cc_final: 0.6670 (m-80)
REVERT: A  385 TYR cc_start: 0.6410 (OUTLIER) cc_final: 0.6087 (t80)
REVERT: A  564 ARG cc_start: 0.8153 (ttt90) cc_final: 0.7645 (ttt90)
REVERT: B   53 MET cc_start: 0.8181 (tpt) cc_final: 0.7542 (mmt)
REVERT: C  116 LYS cc_start: 0.7685 (tttt) cc_final: 0.6371 (mtmt)
  outliers start: 29
  outliers final: 21
  residues processed: 87
  average time/residue: 0.0805
  time to fit residues: 9.3755
Evaluate side-chains
  82 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 60
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  126 ILE
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  197 TRP
Chi-restraints excluded: chain A residue  209 CYS
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  385 TYR
Chi-restraints excluded: chain A residue  396 GLU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain A residue  616 THR
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue  107 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 68 optimal weight:    0.6980
   chunk 69 optimal weight:    0.8980
   chunk 47 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 60 optimal weight:    0.3980
   chunk 71 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0010
   chunk 44 optimal weight:    0.6980
   overall best weight:    0.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 354 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.177337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.156012 restraints weight = 6857.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.156321 restraints weight = 6053.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.158675 restraints weight = 5269.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.159129 restraints weight = 4279.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.159152 restraints weight = 3852.259|
|-----------------------------------------------------------------------------|
r_work (final): 0.3894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.3240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6409  Z= 0.111
  Angle     :  0.525   9.421   8644  Z= 0.264
  Chirality :  0.041   0.262    942
  Planarity :  0.003   0.030   1044
  Dihedral  :  5.119  57.114   1004
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 18.59 %
    Favored  : 77.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.16 (0.32), residues: 761
  helix:  0.72 (0.29), residues: 353
  sheet: -1.29 (0.60), residues: 97
  loop : -2.40 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  38 
 TYR   0.022   0.001   TYR A 176 
 PHE   0.017   0.001   PHE A 423 
 TRP   0.008   0.001   TRP A 197 
 HIS   0.001   0.000   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 6403)
  covalent geometry    : angle       0.52152 ( 8632)
  SS BOND              : bond        0.00220 (    3)
  SS BOND              : angle       1.84988 (    6)
  hydrogen bonds       : bond        0.03258 (  260)
  hydrogen bonds       : angle       4.03803 (  765)
  Misc. bond           : bond        0.00024 (    1)
  link_BETA1-4         : bond        0.00480 (    1)
  link_BETA1-4         : angle       0.71202 (    3)
  link_NAG-ASN         : bond        0.00205 (    1)
  link_NAG-ASN         : angle       2.38027 (    3)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 61
  time to evaluate  : 0.228 
Fit side-chains
REVERT: A  102 VAL cc_start: 0.8731 (p) cc_final: 0.8500 (t)
REVERT: A  564 ARG cc_start: 0.8156 (ttt90) cc_final: 0.7881 (ttt90)
REVERT: B   38 ARG cc_start: 0.7595 (ttp80) cc_final: 0.7122 (ttm-80)
REVERT: C  116 LYS cc_start: 0.7875 (tttt) cc_final: 0.7136 (mtmt)
  outliers start: 26
  outliers final: 21
  residues processed: 83
  average time/residue: 0.0783
  time to fit residues: 8.8222
Evaluate side-chains
  80 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 59
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  126 ILE
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  197 TRP
Chi-restraints excluded: chain A residue  209 CYS
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  396 GLU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain A residue  616 THR
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   70 ILE
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue  107 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 29 optimal weight:    0.0270
   chunk 63 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 71 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.6640

-------------------------------------------------------------------------------
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 = 0.3793 r_free = 0.3793 target = 0.155535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.120461 restraints weight = 7348.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.125965 restraints weight = 4227.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.129646 restraints weight = 2955.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.131863 restraints weight = 2333.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.133706 restraints weight = 2001.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6976
moved from start:          0.3438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6409  Z= 0.126
  Angle     :  0.537   9.409   8644  Z= 0.271
  Chirality :  0.041   0.263    942
  Planarity :  0.004   0.031   1044
  Dihedral  :  5.295  57.245   1004
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 18.12 %
    Favored  : 77.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.10 (0.32), residues: 761
  helix:  0.76 (0.29), residues: 353
  sheet: -1.22 (0.59), residues: 97
  loop : -2.37 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  38 
 TYR   0.023   0.002   TYR A 176 
 PHE   0.014   0.001   PHE A 423 
 TRP   0.008   0.001   TRP B  66 
 HIS   0.001   0.000   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 6403)
  covalent geometry    : angle       0.53343 ( 8632)
  SS BOND              : bond        0.00221 (    3)
  SS BOND              : angle       1.85600 (    6)
  hydrogen bonds       : bond        0.03459 (  260)
  hydrogen bonds       : angle       4.06185 (  765)
  Misc. bond           : bond        0.00033 (    1)
  link_BETA1-4         : bond        0.00386 (    1)
  link_BETA1-4         : angle       0.61808 (    3)
  link_NAG-ASN         : bond        0.00144 (    1)
  link_NAG-ASN         : angle       2.52645 (    3)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 68
  time to evaluate  : 0.243 
Fit side-chains
REVERT: A  145 ASN cc_start: 0.8519 (m110) cc_final: 0.8284 (m-40)
REVERT: A  185 TYR cc_start: 0.8073 (t80) cc_final: 0.7747 (t80)
REVERT: A  306 TRP cc_start: 0.6992 (t-100) cc_final: 0.5742 (p-90)
REVERT: B   38 ARG cc_start: 0.8153 (ttp80) cc_final: 0.7540 (ttm-80)
REVERT: C  116 LYS cc_start: 0.7879 (tttt) cc_final: 0.6373 (mtmt)
  outliers start: 27
  outliers final: 22
  residues processed: 88
  average time/residue: 0.0734
  time to fit residues: 8.8554
Evaluate side-chains
  88 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 66
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  126 ILE
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  197 TRP
Chi-restraints excluded: chain A residue  209 CYS
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  396 GLU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain A residue  616 THR
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  127 MET
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue  107 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 23 optimal weight:    0.0170
   chunk 4 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 72 optimal weight:    6.9990
   chunk 11 optimal weight:    2.9990
   chunk 54 optimal weight:    5.9990
   overall best weight:    1.1422

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
A 112 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.150746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.115603 restraints weight = 7480.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.120906 restraints weight = 4330.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.124512 restraints weight = 3054.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.126952 restraints weight = 2421.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.128358 restraints weight = 2068.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7020
moved from start:          0.3864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6409  Z= 0.181
  Angle     :  0.613   9.388   8644  Z= 0.313
  Chirality :  0.044   0.267    942
  Planarity :  0.004   0.032   1044
  Dihedral  :  5.731  57.409   1002
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.36 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 17.81 %
    Favored  : 77.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.20 (0.32), residues: 761
  helix:  0.69 (0.29), residues: 348
  sheet: -1.40 (0.55), residues: 106
  loop : -2.35 (0.35), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  38 
 TYR   0.026   0.002   TYR A 176 
 PHE   0.015   0.001   PHE A 373 
 TRP   0.038   0.002   TRP A 514 
 HIS   0.002   0.001   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 ( 6403)
  covalent geometry    : angle       0.60869 ( 8632)
  SS BOND              : bond        0.00266 (    3)
  SS BOND              : angle       2.11832 (    6)
  hydrogen bonds       : bond        0.04302 (  260)
  hydrogen bonds       : angle       4.26005 (  765)
  Misc. bond           : bond        0.00064 (    1)
  link_BETA1-4         : bond        0.00216 (    1)
  link_BETA1-4         : angle       0.48234 (    3)
  link_NAG-ASN         : bond        0.00011 (    1)
  link_NAG-ASN         : angle       2.75258 (    3)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 71
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
REVERT: A  107 TYR cc_start: 0.5982 (OUTLIER) cc_final: 0.5512 (t80)
REVERT: A  145 ASN cc_start: 0.8498 (m110) cc_final: 0.8275 (m-40)
REVERT: A  306 TRP cc_start: 0.7042 (t-100) cc_final: 0.5765 (p-90)
REVERT: A  385 TYR cc_start: 0.6709 (OUTLIER) cc_final: 0.6124 (t80)
REVERT: A  388 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7356 (tm-30)
REVERT: B   53 MET cc_start: 0.8260 (tpt) cc_final: 0.7606 (mmt)
REVERT: B   79 TYR cc_start: 0.8927 (m-80) cc_final: 0.8517 (m-80)
  outliers start: 32
  outliers final: 21
  residues processed: 96
  average time/residue: 0.0625
  time to fit residues: 8.2713
Evaluate side-chains
  88 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 65
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  107 TYR
Chi-restraints excluded: chain A residue  126 ILE
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  197 TRP
Chi-restraints excluded: chain A residue  209 CYS
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  385 TYR
Chi-restraints excluded: chain A residue  396 GLU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   70 ILE
Chi-restraints excluded: chain B residue  127 MET
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue  107 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 58 optimal weight:    0.0370
   chunk 70 optimal weight:    3.9990
   chunk 24 optimal weight:    0.0770
   chunk 73 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 52 optimal weight:    0.5980
   chunk 69 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   chunk 4 optimal weight:    0.0270
   chunk 33 optimal weight:    0.8980
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.2874

-------------------------------------------------------------------------------
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 = 0.3808 r_free = 0.3808 target = 0.157053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.121603 restraints weight = 7394.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.127321 restraints weight = 4255.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.131130 restraints weight = 2960.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.133688 restraints weight = 2325.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.135305 restraints weight = 1969.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6860
moved from start:          0.3715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6409  Z= 0.102
  Angle     :  0.537   9.375   8644  Z= 0.273
  Chirality :  0.041   0.256    942
  Planarity :  0.003   0.033   1044
  Dihedral  :  5.108  57.230   1002
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 21.09 %
    Favored  : 76.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.96 (0.32), residues: 761
  helix:  0.77 (0.29), residues: 360
  sheet: -0.83 (0.60), residues: 92
  loop : -2.32 (0.35), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  38 
 TYR   0.025   0.001   TYR A 176 
 PHE   0.015   0.001   PHE A 423 
 TRP   0.023   0.001   TRP A 514 
 HIS   0.001   0.000   HIS A 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 6403)
  covalent geometry    : angle       0.53234 ( 8632)
  SS BOND              : bond        0.00125 (    3)
  SS BOND              : angle       1.83233 (    6)
  hydrogen bonds       : bond        0.03069 (  260)
  hydrogen bonds       : angle       4.07391 (  765)
  Misc. bond           : bond        0.00005 (    1)
  link_BETA1-4         : bond        0.00404 (    1)
  link_BETA1-4         : angle       0.59635 (    3)
  link_NAG-ASN         : bond        0.00258 (    1)
  link_NAG-ASN         : angle       2.66304 (    3)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 70
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A  145 ASN cc_start: 0.8428 (m110) cc_final: 0.8200 (m-40)
REVERT: A  306 TRP cc_start: 0.6951 (t-100) cc_final: 0.5706 (p-90)
REVERT: B   38 ARG cc_start: 0.8142 (ttp80) cc_final: 0.7508 (ttm-80)
REVERT: B   53 MET cc_start: 0.8159 (tpt) cc_final: 0.7549 (mmt)
REVERT: B   79 TYR cc_start: 0.8894 (m-80) cc_final: 0.8418 (m-80)
  outliers start: 18
  outliers final: 16
  residues processed: 84
  average time/residue: 0.0811
  time to fit residues: 9.3217
Evaluate side-chains
  82 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 66
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  197 TRP
Chi-restraints excluded: chain A residue  209 CYS
Chi-restraints excluded: chain A residue  396 GLU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue  107 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0980
   chunk 72 optimal weight:    6.9990
   chunk 4 optimal weight:    0.7980
   chunk 54 optimal weight:    4.9990
   chunk 8 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3785 r_free = 0.3785 target = 0.154810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.119515 restraints weight = 7440.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.125073 restraints weight = 4283.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.128570 restraints weight = 2999.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.131211 restraints weight = 2382.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.132717 restraints weight = 2016.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6898
moved from start:          0.3799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6409  Z= 0.122
  Angle     :  0.563   9.383   8644  Z= 0.284
  Chirality :  0.042   0.263    942
  Planarity :  0.003   0.032   1044
  Dihedral  :  5.169  57.588   1002
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 20.78 %
    Favored  : 75.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.92 (0.32), residues: 761
  helix:  0.82 (0.29), residues: 361
  sheet: -1.07 (0.58), residues: 97
  loop : -2.25 (0.36), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 462 
 TYR   0.026   0.002   TYR A 176 
 PHE   0.011   0.001   PHE A 133 
 TRP   0.026   0.001   TRP A 514 
 HIS   0.001   0.000   HIS A 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 6403)
  covalent geometry    : angle       0.55879 ( 8632)
  SS BOND              : bond        0.00245 (    3)
  SS BOND              : angle       1.87534 (    6)
  hydrogen bonds       : bond        0.03404 (  260)
  hydrogen bonds       : angle       4.09457 (  765)
  Misc. bond           : bond        0.00032 (    1)
  link_BETA1-4         : bond        0.00357 (    1)
  link_BETA1-4         : angle       0.58235 (    3)
  link_NAG-ASN         : bond        0.00137 (    1)
  link_NAG-ASN         : angle       2.71079 (    3)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 72
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A  107 TYR cc_start: 0.5616 (OUTLIER) cc_final: 0.5174 (t80)
REVERT: A  145 ASN cc_start: 0.8461 (m110) cc_final: 0.8240 (m-40)
REVERT: A  204 TRP cc_start: 0.1569 (OUTLIER) cc_final: -0.0270 (m-90)
REVERT: A  306 TRP cc_start: 0.6968 (t-100) cc_final: 0.5725 (p-90)
REVERT: A  385 TYR cc_start: 0.6494 (OUTLIER) cc_final: 0.6058 (t80)
REVERT: B   38 ARG cc_start: 0.8168 (ttp80) cc_final: 0.7517 (ttm-80)
REVERT: B   53 MET cc_start: 0.8174 (tpt) cc_final: 0.7546 (mmt)
REVERT: B   79 TYR cc_start: 0.8897 (m-80) cc_final: 0.8392 (m-80)
  outliers start: 21
  outliers final: 16
  residues processed: 90
  average time/residue: 0.0771
  time to fit residues: 9.5918
Evaluate side-chains
  89 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 70
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  107 TYR
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  197 TRP
Chi-restraints excluded: chain A residue  204 TRP
Chi-restraints excluded: chain A residue  209 CYS
Chi-restraints excluded: chain A residue  385 TYR
Chi-restraints excluded: chain A residue  396 GLU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue  107 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 68 optimal weight:    0.8980
   chunk 63 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 56 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0980
   chunk 64 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3762 r_free = 0.3762 target = 0.152886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.117520 restraints weight = 7464.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.122992 restraints weight = 4296.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.126640 restraints weight = 3027.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.129089 restraints weight = 2399.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.130755 restraints weight = 2046.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6930
moved from start:          0.3871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6409  Z= 0.129
  Angle     :  0.578   9.360   8644  Z= 0.291
  Chirality :  0.043   0.260    942
  Planarity :  0.003   0.032   1044
  Dihedral  :  5.273  57.566   1002
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 20.78 %
    Favored  : 75.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.88 (0.32), residues: 761
  helix:  0.84 (0.28), residues: 361
  sheet: -1.04 (0.59), residues: 97
  loop : -2.21 (0.37), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  38 
 TYR   0.028   0.002   TYR A 176 
 PHE   0.014   0.001   PHE A 423 
 TRP   0.026   0.001   TRP A 514 
 HIS   0.001   0.001   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 6403)
  covalent geometry    : angle       0.57363 ( 8632)
  SS BOND              : bond        0.00233 (    3)
  SS BOND              : angle       1.90081 (    6)
  hydrogen bonds       : bond        0.03475 (  260)
  hydrogen bonds       : angle       4.09866 (  765)
  Misc. bond           : bond        0.00032 (    1)
  link_BETA1-4         : bond        0.00357 (    1)
  link_BETA1-4         : angle       0.59597 (    3)
  link_NAG-ASN         : bond        0.00142 (    1)
  link_NAG-ASN         : angle       2.67733 (    3)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 68
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A  107 TYR cc_start: 0.5760 (OUTLIER) cc_final: 0.5192 (t80)
REVERT: A  145 ASN cc_start: 0.8462 (m110) cc_final: 0.8238 (m-40)
REVERT: A  204 TRP cc_start: 0.1628 (OUTLIER) cc_final: -0.0284 (m-90)
REVERT: A  306 TRP cc_start: 0.6996 (t-100) cc_final: 0.5788 (p-90)
REVERT: A  385 TYR cc_start: 0.6497 (OUTLIER) cc_final: 0.6102 (t80)
REVERT: B   38 ARG cc_start: 0.8193 (ttp80) cc_final: 0.7553 (ttm-80)
REVERT: B   53 MET cc_start: 0.8171 (tpt) cc_final: 0.7512 (mmt)
REVERT: B   79 TYR cc_start: 0.8903 (m-80) cc_final: 0.8404 (m-80)
  outliers start: 21
  outliers final: 18
  residues processed: 86
  average time/residue: 0.0771
  time to fit residues: 9.0813
Evaluate side-chains
  88 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 67
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  107 TYR
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  197 TRP
Chi-restraints excluded: chain A residue  204 TRP
Chi-restraints excluded: chain A residue  209 CYS
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  385 TYR
Chi-restraints excluded: chain A residue  396 GLU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue  107 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program
    task.run()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run
    self.rsr_result = rsr_wrappers.run_real_space_refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__
    self._refined = macro_cycle_real_space.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs
    ro = mmtbx.refinement.real_space.individual_sites.easy(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__
    self.weight = mmtbx.refinement.real_space.weight.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__
    ro.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine
    real_space_result = refinery(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__
    refiner.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine
    self.refined = maptbx.real_space_refinement_simple.lbfgs(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__
    O.minimizer = scitbx.lbfgs.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run
    return run_c_plus_plus(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients
    gr_e = O.geometry_restraints_manager.energies_sites(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites
    pair_proxies = self.pair_proxies(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 58.1129 > 50:
  distance: 50 - 69:  20.597
  distance: 54 - 77:  28.106
  distance: 65 - 69:  21.445
  distance: 69 - 70:  20.225
  distance: 70 - 71:  14.075
  distance: 70 - 73:  15.976
  distance: 71 - 72:  39.608
  distance: 71 - 77:  22.322
  distance: 73 - 74:  30.044
  distance: 74 - 75:   7.234
  distance: 75 - 76:  20.496
  distance: 77 - 78:  11.575
  distance: 78 - 79:   4.725
  distance: 78 - 81:  12.777
  distance: 79 - 80:  11.501
  distance: 79 - 83:  12.482
  distance: 81 - 82:  19.382
  distance: 83 - 84:  21.851
  distance: 83 - 89:  22.699
  distance: 84 - 85:  14.062
  distance: 84 - 87:  14.233
  distance: 85 - 86:   5.420
  distance: 85 - 90:  20.307
  distance: 87 - 88:  15.351
  distance: 88 - 89:  12.829
  distance: 90 - 91:   4.512
  distance: 90 - 96:   6.823
  distance: 91 - 92:   7.685
  distance: 91 - 94:   4.981
  distance: 92 - 93:   5.851
  distance: 92 - 97:   4.186
  distance: 94 - 95:   4.560
  distance: 95 - 96:   5.248
  distance: 98 - 99:   3.049
  distance: 99 - 106:   3.795
  distance: 103 - 104:   3.380
  distance: 103 - 105:   6.968
  distance: 106 - 107:   7.291
  distance: 107 - 108:   8.995
  distance: 107 - 110:   6.360
  distance: 108 - 109:   7.690
  distance: 108 - 114:   4.568
  distance: 110 - 111:  10.965
  distance: 111 - 113:   6.633
  distance: 114 - 115:   3.847
  distance: 115 - 116:  12.034
  distance: 115 - 118:   4.510
  distance: 116 - 117:   6.508
  distance: 116 - 125:   8.146
  distance: 120 - 121:   4.576
  distance: 121 - 122:   4.679
  distance: 122 - 123:   3.376
  distance: 122 - 124:   4.615
  distance: 125 - 126:   8.647
  distance: 126 - 127:  19.990
  distance: 126 - 129:  13.752
  distance: 127 - 128:  16.210
  distance: 127 - 133:  16.635
  distance: 129 - 130:   6.389
  distance: 130 - 131:  13.439
  distance: 130 - 132:  11.681
  distance: 133 - 134:  25.000
  distance: 134 - 135:   8.215
  distance: 134 - 137:  15.358
  distance: 135 - 136:   5.502
  distance: 135 - 144:   6.815
  distance: 137 - 138:  13.411
  distance: 138 - 139:  20.189
  distance: 138 - 140:  12.447
  distance: 139 - 141:   3.918
  distance: 140 - 142:   8.084
  distance: 141 - 143:   5.739
  distance: 142 - 143:  19.859
  distance: 144 - 145:   7.775
  distance: 145 - 146:  16.140
  distance: 145 - 148:  12.659
  distance: 146 - 147:  16.866
  distance: 146 - 153:  21.435
  distance: 149 - 150:   4.801
  distance: 150 - 151:   3.442
  distance: 150 - 152:   3.502