Starting phenix.real_space_refine
on Tue Feb 11 21:33:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7li6_23361/02_2025/7li6_23361.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7li6_23361/02_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7li6_23361/02_2025/7li6_23361.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7li6_23361/02_2025/7li6_23361.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7li6_23361/02_2025/7li6_23361.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7li6_23361/02_2025/7li6_23361.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLU:plan': 1, 'ARG: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: 5.33, per 1000 atoms: 0.85
  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: 1.91
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.95
  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: 1.83

  Time building geometry restraints manager: 2.06 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:             5.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     21.120
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.370
-------------------------------------------------------------------------------
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   0.030   6403  Z= 0.130
  Angle     :  0.667   5.560   8632  Z= 0.305
  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 : 5.37
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.004   0.000   TRP A 282 
 HIS   0.001   0.000   HIS A 223 
 PHE   0.003   0.000   PHE A  88 
 TYR   0.011   0.001   TYR A 175 
 ARG   0.001   0.000   ARG A 234 

*********************** 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  : 0.737 
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: 0.2807
  time to fit residues: 37.8646
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  : 0.655 
-------------------------------------------------------------------------------
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 63 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0980
   chunk 38 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 58 optimal weight:    0.0970
   chunk 22 optimal weight:    0.0470
   chunk 35 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    0.3676

-------------------------------------------------------------------------------
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 416 ASN
A 520 GLN
B  24 GLN
C  98 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.185224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.163780 restraints weight = 6857.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.165458 restraints weight = 5033.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.166610 restraints weight = 4259.962|
|-----------------------------------------------------------------------------|
r_work (final): 0.3947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7360
moved from start:          0.1698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6403  Z= 0.149
  Angle     :  0.517  10.116   8632  Z= 0.261
  Chirality :  0.040   0.246    942
  Planarity :  0.004   0.035   1044
  Dihedral  :  5.160  56.724   1009
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 14.22 %
    Favored  : 82.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.84 (0.30), residues: 761
  helix:  0.29 (0.28), residues: 350
  sheet: -1.79 (0.61), residues: 86
  loop : -2.83 (0.31), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  59 
 HIS   0.001   0.000   HIS A 235 
 PHE   0.008   0.001   PHE A 380 
 TYR   0.022   0.001   TYR A 358 
 ARG   0.007   0.001   ARG A 564 

*********************** 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
  98 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 79
  time to evaluate  : 0.666 
Fit side-chains
   revert: symmetry clash
REVERT: A  301 THR cc_start: 0.7776 (OUTLIER) cc_final: 0.7474 (p)
REVERT: A  370 MET cc_start: 0.7106 (mmp) cc_final: 0.6717 (mmt)
REVERT: C   69 LYS cc_start: 0.7987 (tttp) cc_final: 0.7771 (tttm)
  outliers start: 19
  outliers final: 11
  residues processed: 93
  average time/residue: 0.2184
  time to fit residues: 25.8203
Evaluate side-chains
  75 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.631 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
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  482 THR
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue  118 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 62 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 51 optimal weight:    0.0270
   chunk 21 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.7238

-------------------------------------------------------------------------------
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 = 0.4000 r_free = 0.4000 target = 0.168903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.135342 restraints weight = 7645.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.140347 restraints weight = 4675.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.143649 restraints weight = 3401.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.3721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7390
moved from start:          0.2620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6403  Z= 0.207
  Angle     :  0.539   9.410   8632  Z= 0.275
  Chirality :  0.041   0.266    942
  Planarity :  0.004   0.030   1044
  Dihedral  :  5.018  57.340   1003
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 15.47 %
    Favored  : 80.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.55 (0.31), residues: 761
  helix:  0.50 (0.28), residues: 355
  sheet: -1.73 (0.56), residues: 97
  loop : -2.67 (0.32), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 204 
 HIS   0.002   0.001   HIS A 223 
 PHE   0.014   0.001   PHE A 213 
 TYR   0.022   0.002   TYR A 176 
 ARG   0.004   0.001   ARG A 462 

*********************** 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
  100 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 74
  time to evaluate  : 0.630 
Fit side-chains
   revert: symmetry clash
REVERT: A  306 TRP cc_start: 0.7146 (t-100) cc_final: 0.6244 (p-90)
REVERT: A  370 MET cc_start: 0.7186 (mmp) cc_final: 0.6780 (mmt)
REVERT: A  386 MET cc_start: 0.7309 (ttp) cc_final: 0.7023 (mtm)
REVERT: A  458 TRP cc_start: 0.8238 (m100) cc_final: 0.7815 (m100)
REVERT: B   53 MET cc_start: 0.8268 (tpt) cc_final: 0.8012 (mmt)
  outliers start: 26
  outliers final: 16
  residues processed: 92
  average time/residue: 0.1991
  time to fit residues: 24.4748
Evaluate side-chains
  88 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
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  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  481 LEU
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain C residue   82 VAL
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 54 optimal weight:    5.9990
   chunk 14 optimal weight:    0.4980
   chunk 61 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9990
   chunk 60 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 68 optimal weight:    0.0980
   chunk 66 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3980 r_free = 0.3980 target = 0.167408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.133055 restraints weight = 7877.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.138357 restraints weight = 4645.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.141866 restraints weight = 3318.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7443
moved from start:          0.3023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6403  Z= 0.188
  Angle     :  0.546   9.493   8632  Z= 0.273
  Chirality :  0.041   0.257    942
  Planarity :  0.004   0.030   1044
  Dihedral  :  5.086  56.643   1003
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 17.03 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.25 (0.31), residues: 761
  helix:  0.65 (0.28), residues: 355
  sheet: -1.39 (0.59), residues: 97
  loop : -2.45 (0.34), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 541 
 HIS   0.001   0.001   HIS A 235 
 PHE   0.011   0.001   PHE A 213 
 TYR   0.025   0.001   TYR A 176 
 ARG   0.004   0.000   ARG A 462 

*********************** 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
  93 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 65
  time to evaluate  : 0.634 
Fit side-chains
REVERT: A  152 ARG cc_start: 0.8541 (tpp80) cc_final: 0.8191 (tpp80)
REVERT: A  247 ASP cc_start: 0.8455 (t0) cc_final: 0.8226 (t0)
REVERT: A  370 MET cc_start: 0.7200 (mmp) cc_final: 0.6843 (mmt)
REVERT: A  386 MET cc_start: 0.7241 (ttp) cc_final: 0.7014 (mtm)
REVERT: A  564 ARG cc_start: 0.7722 (ttt-90) cc_final: 0.7451 (ttt-90)
  outliers start: 28
  outliers final: 22
  residues processed: 87
  average time/residue: 0.1881
  time to fit residues: 21.8021
Evaluate side-chains
  84 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 62
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
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  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  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  481 LEU
Chi-restraints excluded: chain A residue  482 THR
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   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   40 THR
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 59 optimal weight:    0.1980
   chunk 4 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 73 optimal weight:    0.6980
   chunk 72 optimal weight:    7.9990
   chunk 74 optimal weight:    0.0670
   chunk 12 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 51 optimal weight:    0.4980
   chunk 41 optimal weight:    0.0870
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.2896

-------------------------------------------------------------------------------
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 = 0.3868 r_free = 0.3868 target = 0.163105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.127162 restraints weight = 7309.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.133012 restraints weight = 4210.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.136914 restraints weight = 2940.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6806
moved from start:          0.3071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6403  Z= 0.135
  Angle     :  0.510   9.418   8632  Z= 0.255
  Chirality :  0.040   0.261    942
  Planarity :  0.003   0.030   1044
  Dihedral  :  4.885  57.349   1003
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 17.81 %
    Favored  : 78.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.06 (0.32), residues: 761
  helix:  0.72 (0.28), residues: 361
  sheet: -0.94 (0.61), residues: 92
  loop : -2.42 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 197 
 HIS   0.002   0.001   HIS C 100 
 PHE   0.017   0.001   PHE A 347 
 TYR   0.020   0.001   TYR A 176 
 ARG   0.003   0.000   ARG A 462 

*********************** 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
  88 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 64
  time to evaluate  : 0.583 
Fit side-chains
REVERT: A  102 VAL cc_start: 0.8383 (p) cc_final: 0.8182 (t)
REVERT: A  107 TYR cc_start: 0.5473 (OUTLIER) cc_final: 0.4693 (t80)
REVERT: A  247 ASP cc_start: 0.8316 (t0) cc_final: 0.8027 (t0)
REVERT: A  370 MET cc_start: 0.6556 (mmp) cc_final: 0.6229 (mmt)
REVERT: A  385 TYR cc_start: 0.6187 (OUTLIER) cc_final: 0.5953 (t80)
REVERT: A  564 ARG cc_start: 0.7472 (ttt-90) cc_final: 0.7153 (ttt-90)
REVERT: B   53 MET cc_start: 0.8187 (tpt) cc_final: 0.7509 (mmt)
  outliers start: 24
  outliers final: 17
  residues processed: 84
  average time/residue: 0.1950
  time to fit residues: 21.9293
Evaluate side-chains
  78 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 59
  time to evaluate  : 0.633 
-------------------------------------------------------------------------------
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  107 TYR
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 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   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 43 optimal weight:    0.9990
   chunk 27 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   chunk 19 optimal weight:    0.2980
   chunk 11 optimal weight:    0.7980
   chunk 10 optimal weight:    0.5980
   chunk 22 optimal weight:    6.9990
   chunk 66 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.6582

-------------------------------------------------------------------------------
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 = 0.4169 r_free = 0.4169 target = 0.189319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.166298 restraints weight = 6527.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.166906 restraints weight = 5878.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.168618 restraints weight = 4981.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.3365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6403  Z= 0.197
  Angle     :  0.537   9.409   8632  Z= 0.270
  Chirality :  0.042   0.262    942
  Planarity :  0.003   0.032   1044
  Dihedral  :  5.181  57.265   1003
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 18.28 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.01 (0.32), residues: 761
  helix:  0.85 (0.28), residues: 353
  sheet: -1.13 (0.59), residues: 97
  loop : -2.35 (0.35), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 204 
 HIS   0.001   0.000   HIS A 223 
 PHE   0.016   0.001   PHE A 423 
 TYR   0.022   0.001   TYR A 176 
 ARG   0.007   0.001   ARG A 152 

*********************** 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
  91 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 68
  time to evaluate  : 0.698 
Fit side-chains
REVERT: A  102 VAL cc_start: 0.8802 (p) cc_final: 0.8560 (t)
REVERT: A  306 TRP cc_start: 0.7255 (t-100) cc_final: 0.6789 (p-90)
REVERT: A  370 MET cc_start: 0.7300 (mmp) cc_final: 0.7053 (mmt)
  outliers start: 23
  outliers final: 18
  residues processed: 87
  average time/residue: 0.1762
  time to fit residues: 21.2115
Evaluate side-chains
  84 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 66
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
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 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  127 MET
Chi-restraints excluded: chain B residue  137 THR
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 19 optimal weight:    0.0370
   chunk 18 optimal weight:    0.6980
   chunk 37 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 73 optimal weight:    0.6980
   chunk 63 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 44 optimal weight:    0.8980
   chunk 20 optimal weight:    9.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.6258

-------------------------------------------------------------------------------
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 = 0.3811 r_free = 0.3811 target = 0.157660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.122057 restraints weight = 7388.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.127634 restraints weight = 4348.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.131378 restraints weight = 3072.079|
|-----------------------------------------------------------------------------|
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6905
moved from start:          0.3504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6403  Z= 0.191
  Angle     :  0.538   9.395   8632  Z= 0.273
  Chirality :  0.042   0.260    942
  Planarity :  0.003   0.033   1044
  Dihedral  :  4.987  57.264   1001
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 18.91 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.32), residues: 761
  helix:  0.87 (0.29), residues: 354
  sheet: -0.76 (0.61), residues: 92
  loop : -2.35 (0.35), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP A 514 
 HIS   0.001   0.000   HIS A 223 
 PHE   0.010   0.001   PHE A 423 
 TYR   0.025   0.001   TYR A 176 
 ARG   0.006   0.000   ARG A 152 

*********************** 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
  90 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 68
  time to evaluate  : 0.660 
Fit side-chains
REVERT: A  145 ASN cc_start: 0.8595 (m110) cc_final: 0.8294 (m-40)
REVERT: A  306 TRP cc_start: 0.6933 (t-100) cc_final: 0.5770 (p-90)
REVERT: A  370 MET cc_start: 0.6613 (mmp) cc_final: 0.6286 (mmt)
REVERT: B   38 ARG cc_start: 0.7787 (ttm-80) cc_final: 0.7224 (ttm-80)
REVERT: B   53 MET cc_start: 0.8254 (tpt) cc_final: 0.7564 (mmt)
  outliers start: 22
  outliers final: 19
  residues processed: 86
  average time/residue: 0.1619
  time to fit residues: 19.3623
Evaluate side-chains
  82 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 63
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  101 ASN
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  127 MET
Chi-restraints excluded: chain B residue  137 THR
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 6 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   chunk 68 optimal weight:    0.1980
   chunk 13 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 35 optimal weight:    0.5980
   chunk 74 optimal weight:    0.4980
   chunk 41 optimal weight:    0.0870
   overall best weight:    0.4158

-------------------------------------------------------------------------------
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 = 0.3988 r_free = 0.3988 target = 0.168197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.146135 restraints weight = 7065.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.147192 restraints weight = 5622.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.148769 restraints weight = 4948.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.3538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   6403  Z= 0.158
  Angle     :  0.539   9.385   8632  Z= 0.272
  Chirality :  0.041   0.258    942
  Planarity :  0.003   0.032   1044
  Dihedral  :  4.865  57.386   1001
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 20.16 %
    Favored  : 76.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.32), residues: 761
  helix:  0.87 (0.28), residues: 361
  sheet: -0.67 (0.61), residues: 92
  loop : -2.32 (0.36), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 514 
 HIS   0.001   0.000   HIS A 235 
 PHE   0.012   0.001   PHE A 133 
 TYR   0.025   0.001   TYR A 110 
 ARG   0.006   0.000   ARG A 152 

*********************** 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
  84 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 63
  time to evaluate  : 0.641 
Fit side-chains
   revert: symmetry clash
REVERT: A  370 MET cc_start: 0.7226 (mmp) cc_final: 0.6998 (mmt)
REVERT: B   53 MET cc_start: 0.8128 (tpt) cc_final: 0.7922 (mmt)
  outliers start: 21
  outliers final: 19
  residues processed: 80
  average time/residue: 0.1833
  time to fit residues: 19.8597
Evaluate side-chains
  78 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 59
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
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  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  103 SER
Chi-restraints excluded: chain B residue  137 THR
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 62 optimal weight:    0.5980
   chunk 19 optimal weight:    0.5980
   chunk 46 optimal weight:    0.8980
   chunk 60 optimal weight:    0.4980
   chunk 8 optimal weight:    0.6980
   chunk 70 optimal weight:    0.0670
   chunk 27 optimal weight:    3.9990
   chunk 69 optimal weight:    0.0770
   chunk 50 optimal weight:    0.6980
   chunk 6 optimal weight:    0.5980
   chunk 54 optimal weight:    5.9990
   overall best weight:    0.3676

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.169335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.147443 restraints weight = 7106.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.148324 restraints weight = 5632.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.150496 restraints weight = 4950.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.3545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6403  Z= 0.151
  Angle     :  0.532   9.365   8632  Z= 0.269
  Chirality :  0.041   0.258    942
  Planarity :  0.003   0.032   1044
  Dihedral  :  4.802  57.478   1001
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 19.69 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.32), residues: 761
  helix:  0.95 (0.28), residues: 361
  sheet: -0.64 (0.62), residues: 92
  loop : -2.30 (0.36), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 514 
 HIS   0.001   0.000   HIS A 143 
 PHE   0.011   0.001   PHE A 133 
 TYR   0.022   0.001   TYR A 176 
 ARG   0.005   0.000   ARG A 152 

*********************** 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
  81 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 61
  time to evaluate  : 0.644 
Fit side-chains
   revert: symmetry clash
REVERT: A  370 MET cc_start: 0.7246 (mmp) cc_final: 0.7033 (mmt)
  outliers start: 20
  outliers final: 19
  residues processed: 79
  average time/residue: 0.1836
  time to fit residues: 19.6036
Evaluate side-chains
  78 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 59
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  175 TYR
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  502 LEU
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   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 2 optimal weight:    0.5980
   chunk 38 optimal weight:    0.0270
   chunk 59 optimal weight:    0.5980
   chunk 69 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   chunk 24 optimal weight:    0.3980
   overall best weight:    0.4838

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.168384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.146109 restraints weight = 7105.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.146742 restraints weight = 5717.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.149018 restraints weight = 5084.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.3630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6403  Z= 0.171
  Angle     :  0.544   9.372   8632  Z= 0.275
  Chirality :  0.041   0.259    942
  Planarity :  0.003   0.032   1044
  Dihedral  :  4.887  57.556   1001
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 19.84 %
    Favored  : 77.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (0.32), residues: 761
  helix:  0.96 (0.28), residues: 361
  sheet: -0.61 (0.62), residues: 92
  loop : -2.26 (0.36), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 514 
 HIS   0.001   0.000   HIS A 223 
 PHE   0.011   0.001   PHE A 133 
 TYR   0.025   0.001   TYR A 110 
 ARG   0.005   0.000   ARG A 152 

********************** 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
  85 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 65
  time to evaluate  : 0.560 
Fit side-chains
   revert: symmetry clash
REVERT: A  370 MET cc_start: 0.7301 (mmp) cc_final: 0.7074 (mmt)
  outliers start: 20
  outliers final: 19
  residues processed: 82
  average time/residue: 0.1923
  time to fit residues: 21.3481
Evaluate side-chains
  82 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 63
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  175 TYR
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  103 SER
Chi-restraints excluded: chain B residue  137 THR
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 18 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 12 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 59 optimal weight:    0.0980
   chunk 23 optimal weight:    0.4980
   chunk 32 optimal weight:    0.0770
   chunk 67 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   overall best weight:    0.4538

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.168258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.146209 restraints weight = 7245.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.147249 restraints weight = 5749.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.149223 restraints weight = 5046.503|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.3673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6403  Z= 0.167
  Angle     :  0.546   9.371   8632  Z= 0.275
  Chirality :  0.041   0.257    942
  Planarity :  0.003   0.033   1044
  Dihedral  :  4.857  57.604   1001
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 19.69 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.32), residues: 761
  helix:  1.05 (0.28), residues: 361
  sheet: -0.57 (0.61), residues: 92
  loop : -2.19 (0.37), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 514 
 HIS   0.001   0.000   HIS A 223 
 PHE   0.011   0.001   PHE A 133 
 TYR   0.023   0.001   TYR A 176 
 ARG   0.005   0.000   ARG A 152 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2248.40 seconds
wall clock time: 41 minutes 27.00 seconds (2487.00 seconds total)