Starting phenix.real_space_refine
on Tue Feb 11 20:55:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7li8_23363/02_2025/7li8_23363.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7li8_23363/02_2025/7li8_23363.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7li8_23363/02_2025/7li8_23363.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7li8_23363/02_2025/7li8_23363.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7li8_23363/02_2025/7li8_23363.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7li8_23363/02_2025/7li8_23363.cif"
  }
  resolution = 3.9
  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=   0.000 sd=   0.025
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      34      5.16       5
     C    4104      2.51       5
     N     962      2.21       5
     O    1081      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6181
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4303
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 539, 4303
          Classifications: {'peptide': 539}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 23, 'TRANS': 515}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    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: 109
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 109
          Unusual residues: {'D10': 1, 'D12': 3, 'HP6': 6, 'LNK': 1, 'R16': 1}
          Classifications: {'undetermined': 12}
          Link IDs: {None: 11}
  Time building chain proxies: 6.92, per 1000 atoms: 1.12
  Number of scatterers: 6181
  At special positions: 0
  Unit cell: (68.688, 77.112, 122.472, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      34     16.00
     O    1081      8.00
     N     962      7.00
     C    4104      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: 1.69
  Conformation dependent library (CDL) restraints added in 887.7 milliseconds
  

  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:
      31 helices and 8 sheets defined
      51.0% alpha, 9.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 83 through 91
    Processing helix  chain 'A' and resid 98 through 103
    Processing helix  chain 'A' and resid 103 through 112
      removed outlier: 3.679A  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 148 through 153
    Processing helix  chain 'A' and resid 159 through 176
      removed outlier: 4.107A  pdb=" N   TYR A 163 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 190
      removed outlier: 4.028A  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: 3.628A  pdb=" N   CYS A 258 " --> pdb=" O   GLN A 254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 286
      removed outlier: 3.769A  pdb=" N   VAL A 283 " --> pdb=" O   LYS A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 301
      removed outlier: 4.317A  pdb=" N   SER A 293 " --> pdb=" O   TYR A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 313
    Processing helix  chain 'A' and resid 316 through 320
    Processing helix  chain 'A' and resid 325 through 338
      removed outlier: 3.660A  pdb=" N   GLY A 338 " --> pdb=" O   PHE A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 349
    Processing helix  chain 'A' and resid 359 through 389
      removed outlier: 3.988A  pdb=" N   VAL A 382 " --> pdb=" O   VAL A 378 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   TYR A 385 " --> pdb=" O   THR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 397
      removed outlier: 3.802A  pdb=" N   VAL A 397 " --> pdb=" O   VAL A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 415
      removed outlier: 4.411A  pdb=" N   PHE A 407 " --> pdb=" O   PRO A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 448
      removed outlier: 4.117A  pdb=" N   ALA A 441 " --> pdb=" O   ASP A 437 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   GLY A 442 " --> pdb=" O   SER A 438 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   LEU A 443 " --> pdb=" O   THR A 439 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   GLY A 445 " --> pdb=" O   ALA A 441 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   VAL A 446 " --> pdb=" O   GLY A 442 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   THR A 448 " --> pdb=" O   GLU A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 477
    Processing helix  chain 'A' and resid 478 through 482
      removed outlier: 3.842A  pdb=" N   THR A 482 " --> pdb=" O   VAL A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 485 through 496
      removed outlier: 4.382A  pdb=" N   LEU A 491 " --> pdb=" O   TYR A 487 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   GLU A 494 " --> pdb=" O   LYS A 490 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ALA A 496 " --> pdb=" O   LEU A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 515
      removed outlier: 3.769A  pdb=" N   LEU A 502 " --> pdb=" O   GLY A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 530
    Processing helix  chain 'A' and resid 534 through 558
      removed outlier: 3.641A  pdb=" N   ARG A 538 " --> pdb=" O   GLY A 534 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   TRP A 541 " --> pdb=" O   TRP A 537 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   VAL A 542 " --> pdb=" O   ARG A 538 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ALA A 543 " --> pdb=" O   ILE A 539 " (cutoff:3.500A)
      removed outlier: 5.707A  pdb=" N   SER A 545 " --> pdb=" O   TRP A 541 " (cutoff:3.500A)
      Proline residue:  A 546  - end of helix
    Processing helix  chain 'A' and resid 571 through 585
      removed outlier: 4.187A  pdb=" N   ILE A 575 " --> pdb=" O   PRO A 571 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ILE A 576 " --> pdb=" O   TYR A 572 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   SER A 585 " --> pdb=" O   ILE A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 598
      removed outlier: 3.813A  pdb=" N   ILE A 598 " --> pdb=" O   ALA A 594 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 613
      removed outlier: 3.743A  pdb=" N   THR A 613 " --> pdb=" O   ILE A 609 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 51
      removed outlier: 4.165A  pdb=" N   TYR B  50 " --> pdb=" O   ARG B  47 " (cutoff:3.500A)
      removed outlier: 3.956A  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 helix  chain 'C' and resid 103 through 107
      removed outlier: 3.519A  pdb=" N   THR C 107 " --> pdb=" O   GLU C 104 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 564 through 565
    Processing sheet with id=AA2, first strand: chain 'B' and resid 22 through 25
      removed outlier: 3.633A  pdb=" N   GLN B  24 " --> pdb=" O   LYS B  42 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   LYS B  42 " --> pdb=" O   GLN B  24 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ILE B  39 " --> pdb=" O   MET B 100 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   MET B 100 " --> pdb=" O   ILE B  39 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 77 through 79
      removed outlier: 3.526A  pdb=" N   ILE B  67 " --> pdb=" O   TRP B  55 " (cutoff:3.500A)
      removed outlier: 7.389A  pdb=" N   TRP B  55 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
      removed outlier: 5.122A  pdb=" N   ARG B  69 " --> pdb=" O   MET B  53 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   MET B  53 " --> pdb=" O   ARG B  69 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 77 through 79
      removed outlier: 3.526A  pdb=" N   ILE B  67 " --> pdb=" O   TRP B  55 " (cutoff:3.500A)
      removed outlier: 7.389A  pdb=" N   TRP B  55 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
      removed outlier: 5.122A  pdb=" N   ARG B  69 " --> pdb=" O   MET B  53 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   MET B  53 " --> pdb=" O   ARG B  69 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 30 through 31
    Processing sheet with id=AA6, first strand: chain 'C' and resid 77 through 78
      removed outlier: 3.774A  pdb=" N   TYR C  73 " --> pdb=" O   ASN C  77 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   TRP C  59 " --> pdb=" O   LEU C  71 " (cutoff:3.500A)
      removed outlier: 5.123A  pdb=" N   TYR C  73 " --> pdb=" O   LEU C  57 " (cutoff:3.500A)
      removed outlier: 7.051A  pdb=" N   LEU C  57 " --> pdb=" O   TYR C  73 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 77 through 78
      removed outlier: 3.774A  pdb=" N   TYR C  73 " --> pdb=" O   ASN C  77 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   TRP C  59 " --> pdb=" O   LEU C  71 " (cutoff:3.500A)
      removed outlier: 5.123A  pdb=" N   TYR C  73 " --> pdb=" O   LEU C  57 " (cutoff:3.500A)
      removed outlier: 7.051A  pdb=" N   LEU C  57 " --> pdb=" O   TYR C  73 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 87 through 90
      removed outlier: 3.561A  pdb=" N   SER C  89 " --> pdb=" O   SER C  96 " (cutoff:3.500A)

    273 hydrogen bonds defined for protein.
    756 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: 1.73

  Time building geometry restraints manager: 1.90 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1811
        1.34 -     1.46: 1452
        1.46 -     1.58: 3037
        1.58 -     1.69: 0
        1.69 -     1.81: 49
  Bond restraints: 6349
  Sorted by residual:
  bond pdb=" C1  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.35e+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 1.56e+00
  bond pdb=" C1  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.430 -0.024 2.00e-02 2.50e+03 1.50e+00
  bond pdb=" C5  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.436 -0.023 2.00e-02 2.50e+03 1.33e+00
  bond pdb=" C5  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.24e+00
  ... (remaining 6344 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.08: 8193
        1.08 -     2.16: 247
        2.16 -     3.24: 65
        3.24 -     4.32: 79
        4.32 -     5.40: 12
  Bond angle restraints: 8596
  Sorted by residual:
  angle pdb=" N   VAL A 102 "
        pdb=" CA  VAL A 102 "
        pdb=" C   VAL A 102 "
      ideal   model   delta    sigma   weight residual
     113.53  109.27    4.26 9.80e-01 1.04e+00 1.89e+01
  angle pdb=" N   VAL A  92 "
        pdb=" CA  VAL A  92 "
        pdb=" C   VAL A  92 "
      ideal   model   delta    sigma   weight residual
     113.71  110.54    3.17 9.50e-01 1.11e+00 1.11e+01
  angle pdb=" N   VAL A 446 "
        pdb=" CA  VAL A 446 "
        pdb=" C   VAL A 446 "
      ideal   model   delta    sigma   weight residual
     112.96  109.70    3.26 1.00e+00 1.00e+00 1.07e+01
  angle pdb=" C   GLY B 121 "
        pdb=" N   SER B 122 "
        pdb=" CA  SER B 122 "
      ideal   model   delta    sigma   weight residual
     120.38  124.54   -4.16 1.37e+00 5.33e-01 9.22e+00
  angle pdb=" C   MET B 127 "
        pdb=" N   ASP B 128 "
        pdb=" CA  ASP B 128 "
      ideal   model   delta    sigma   weight residual
     121.54  126.14   -4.60 1.91e+00 2.74e-01 5.79e+00
  ... (remaining 8591 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.73: 3326
       14.73 -    29.46: 272
       29.46 -    44.19: 59
       44.19 -    58.91: 9
       58.91 -    73.64: 2
  Dihedral angle restraints: 3668
    sinusoidal: 1462
      harmonic: 2206
  Sorted by residual:
  dihedral pdb=" CB  CYS B  41 "
           pdb=" SG  CYS B  41 "
           pdb=" SG  CYS B 115 "
           pdb=" CB  CYS B 115 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  166.64  -73.64     1      1.00e+01 1.00e-02 6.90e+01
  dihedral pdb=" CA  TRP A 204 "
           pdb=" C   TRP A 204 "
           pdb=" N   ASN A 205 "
           pdb=" CA  ASN A 205 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.98   22.02     0      5.00e+00 4.00e-02 1.94e+01
  dihedral pdb=" CA  ASP A  87 "
           pdb=" CB  ASP A  87 "
           pdb=" CG  ASP A  87 "
           pdb=" OD1 ASP A  87 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -82.66   52.66     1      2.00e+01 2.50e-03 9.44e+00
  ... (remaining 3665 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.103: 929
       0.103 -    0.206: 12
       0.206 -    0.309: 0
       0.309 -    0.413: 0
       0.413 -    0.516: 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   -1.88   -0.52 2.00e-02 2.50e+03 6.65e+02
  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 7.05e-01
  chirality pdb=" CB  THR C 107 "
            pdb=" CA  THR C 107 "
            pdb=" OG1 THR C 107 "
            pdb=" CG2 THR C 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.42    0.13 2.00e-01 2.50e+01 4.17e-01
  ... (remaining 939 not shown)

  Planarity restraints: 1048
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 338 "   -0.022 5.00e-02 4.00e+02   3.30e-02 1.74e+00
        pdb=" N   PRO A 339 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO A 339 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 339 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 130 "    0.019 5.00e-02 4.00e+02   2.88e-02 1.33e+00
        pdb=" N   PRO A 131 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO A 131 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 131 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 128 "   -0.005 2.00e-02 2.50e+03   1.07e-02 1.15e+00
        pdb=" C   ASP B 128 "    0.019 2.00e-02 2.50e+03
        pdb=" O   ASP B 128 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   TYR B 129 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 1045 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1068
        2.76 -     3.30: 5736
        3.30 -     3.83: 9932
        3.83 -     4.37: 10836
        4.37 -     4.90: 19149
  Nonbonded interactions: 46721
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 110 "
            pdb=" O   VAL A 394 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" OG  SER B  49 "
            pdb=" O   PRO B  72 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" O   LYS A 201 "
            pdb=" NE1 TRP B  52 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" O   SER A 477 "
            pdb=" OG  SER A 477 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" OG  SER B  36 "
            pdb=" O   LEU B 102 "
     model   vdw
     2.330 3.040
  ... (remaining 46716 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:             8.990
  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:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     21.060
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  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:3.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6990
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   0.031   6349  Z= 0.132
  Angle     :  0.601   5.403   8596  Z= 0.300
  Chirality :  0.041   0.516    942
  Planarity :  0.003   0.033   1047
  Dihedral  : 10.905  69.682   2259
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  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: -3.23 (0.27), residues: 761
  helix: -1.23 (0.23), residues: 353
  sheet: -2.94 (0.51), residues: 82
  loop : -2.92 (0.31), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.000   TRP A 204 
 HIS   0.001   0.000   HIS A 223 
 PHE   0.013   0.000   PHE B 125 
 TYR   0.011   0.001   TYR A 175 
 ARG   0.001   0.000   ARG A 298 

*********************** 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
  153 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.614 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.6008 (mmpt) cc_final: 0.5241 (ptmt)
REVERT: A  152 ARG cc_start: 0.8690 (mmm-85) cc_final: 0.8428 (mmt90)
REVERT: A  222 LEU cc_start: 0.7905 (tp) cc_final: 0.7315 (tp)
REVERT: B   58 GLN cc_start: 0.8476 (tt0) cc_final: 0.8096 (tt0)
REVERT: C   62 GLN cc_start: 0.8044 (tt0) cc_final: 0.7838 (tt0)
REVERT: C  110 TYR cc_start: 0.7845 (m-80) cc_final: 0.7568 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 0.2120
  time to fit residues: 40.9925
Evaluate side-chains
  117 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 19 optimal weight:    6.9990
   chunk 38 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 58 optimal weight:    3.9990
   chunk 22 optimal weight:    7.9990
   chunk 35 optimal weight:    3.9990
   chunk 43 optimal weight:    7.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN
A 194 GLN
A 354 ASN
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.154525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.119960 restraints weight = 10096.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.123953 restraints weight = 6384.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.126658 restraints weight = 4760.744|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.2602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   6349  Z= 0.317
  Angle     :  0.642   9.650   8596  Z= 0.323
  Chirality :  0.042   0.230    942
  Planarity :  0.004   0.032   1047
  Dihedral  :  4.993  57.891    946
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 12.60 %
    Favored  : 83.83 %
  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: -1.99 (0.30), residues: 761
  helix: -0.28 (0.26), residues: 349
  sheet: -2.64 (0.51), residues: 92
  loop : -2.00 (0.37), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 271 
 HIS   0.004   0.001   HIS C 100 
 PHE   0.030   0.002   PHE A 287 
 TYR   0.024   0.002   TYR A 358 
 ARG   0.006   0.001   ARG B  59 

*********************** 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
  144 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 121
  time to evaluate  : 0.676 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.6030 (mmpt) cc_final: 0.5208 (ptmt)
REVERT: A  145 ASN cc_start: 0.8014 (OUTLIER) cc_final: 0.7810 (t0)
REVERT: A  222 LEU cc_start: 0.8041 (tp) cc_final: 0.7787 (tp)
REVERT: A  548 PHE cc_start: 0.7917 (m-80) cc_final: 0.7654 (t80)
REVERT: A  592 TYR cc_start: 0.8682 (t80) cc_final: 0.8414 (t80)
REVERT: B   53 MET cc_start: 0.7463 (ttm) cc_final: 0.7222 (ttm)
REVERT: C  110 TYR cc_start: 0.7906 (m-80) cc_final: 0.7695 (m-80)
  outliers start: 23
  outliers final: 19
  residues processed: 134
  average time/residue: 0.1892
  time to fit residues: 33.0883
Evaluate side-chains
  124 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  127 PHE
Chi-restraints excluded: chain A residue  145 ASN
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  263 PHE
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  446 VAL
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  518 ILE
Chi-restraints excluded: chain A residue  553 ILE
Chi-restraints excluded: chain A residue  604 PHE
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue  104 GLU
Chi-restraints excluded: chain C residue  126 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 6 optimal weight:    0.1980
   chunk 45 optimal weight:    8.9990
   chunk 55 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 58 optimal weight:    0.7980
   chunk 68 optimal weight:    0.0870
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  20 GLN ** 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 = 0.4112 r_free = 0.4112 target = 0.156531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.122395 restraints weight = 10263.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.126441 restraints weight = 6527.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.129152 restraints weight = 4887.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.3784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7417
moved from start:          0.2893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6349  Z= 0.175
  Angle     :  0.577   9.449   8596  Z= 0.286
  Chirality :  0.040   0.240    942
  Planarity :  0.004   0.030   1047
  Dihedral  :  4.772  57.646    946
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 16.49 %
    Favored  : 79.63 %
  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: -1.36 (0.31), residues: 761
  helix:  0.27 (0.28), residues: 348
  sheet: -1.88 (0.56), residues: 86
  loop : -1.90 (0.37), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 271 
 HIS   0.002   0.001   HIS A 223 
 PHE   0.018   0.001   PHE A 377 
 TYR   0.037   0.002   TYR A 358 
 ARG   0.006   0.001   ARG C  85 

*********************** 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
  141 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 116
  time to evaluate  : 0.708 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.6079 (mmpt) cc_final: 0.5201 (ptmt)
REVERT: A  222 LEU cc_start: 0.7983 (tp) cc_final: 0.7752 (tp)
REVERT: A  260 MET cc_start: 0.7637 (tmm) cc_final: 0.7281 (tmt)
REVERT: A  370 MET cc_start: 0.8188 (tpp) cc_final: 0.7921 (tpp)
REVERT: A  548 PHE cc_start: 0.7850 (m-80) cc_final: 0.7629 (t80)
REVERT: A  592 TYR cc_start: 0.8666 (t80) cc_final: 0.8427 (t80)
REVERT: C  110 TYR cc_start: 0.7803 (m-80) cc_final: 0.7460 (m-10)
  outliers start: 25
  outliers final: 16
  residues processed: 133
  average time/residue: 0.1765
  time to fit residues: 31.4510
Evaluate side-chains
  119 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  127 PHE
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  263 PHE
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  446 VAL
Chi-restraints excluded: chain A residue  518 ILE
Chi-restraints excluded: chain A residue  604 PHE
Chi-restraints excluded: chain C residue  104 GLU
Chi-restraints excluded: chain C residue  118 VAL
Chi-restraints excluded: chain C residue  126 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    4.9990
   chunk 59 optimal weight:    0.3980
   chunk 65 optimal weight:    7.9990
   chunk 51 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 0 optimal weight:   30.0000
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** B  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 GLN ** 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 = 0.4084 r_free = 0.4084 target = 0.154657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.120479 restraints weight = 10546.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.124558 restraints weight = 6709.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.127310 restraints weight = 5015.629|
|-----------------------------------------------------------------------------|
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
moved from start:          0.3160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6349  Z= 0.194
  Angle     :  0.571   9.452   8596  Z= 0.284
  Chirality :  0.041   0.242    942
  Planarity :  0.004   0.031   1047
  Dihedral  :  4.788  58.387    946
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 17.42 %
    Favored  : 78.85 %
  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:  0.36 (0.28), residues: 350
  sheet: -1.64 (0.57), residues: 85
  loop : -1.91 (0.36), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 535 
 HIS   0.001   0.000   HIS A 223 
 PHE   0.020   0.001   PHE A 377 
 TYR   0.028   0.002   TYR B 120 
 ARG   0.005   0.001   ARG A 538 

*********************** 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
  134 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 110
  time to evaluate  : 0.792 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.6039 (mmpt) cc_final: 0.5180 (ptmt)
REVERT: A  260 MET cc_start: 0.7697 (tmm) cc_final: 0.7298 (tmt)
REVERT: A  370 MET cc_start: 0.8245 (tpp) cc_final: 0.8008 (tpp)
REVERT: A  548 PHE cc_start: 0.7914 (m-80) cc_final: 0.7708 (t80)
REVERT: C  102 MET cc_start: 0.7559 (tmm) cc_final: 0.7173 (tmm)
REVERT: C  105 ASP cc_start: 0.8010 (t0) cc_final: 0.7798 (t0)
REVERT: C  110 TYR cc_start: 0.7902 (m-80) cc_final: 0.7496 (m-10)
  outliers start: 24
  outliers final: 20
  residues processed: 128
  average time/residue: 0.1837
  time to fit residues: 31.2893
Evaluate side-chains
  124 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  204 TRP
Chi-restraints excluded: chain A residue  263 PHE
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  446 VAL
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  604 PHE
Chi-restraints excluded: chain B residue  101 GLN
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  104 GLU
Chi-restraints excluded: chain C residue  118 VAL
Chi-restraints excluded: chain C residue  126 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 52 optimal weight:    6.9990
   chunk 2 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0980
   chunk 46 optimal weight:    5.9990
   chunk 18 optimal weight:    0.8980
   chunk 64 optimal weight:    0.0270
   chunk 20 optimal weight:    0.0020
   chunk 25 optimal weight:    0.7980
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:   10.0000
   chunk 21 optimal weight:    0.5980
   overall best weight:    0.3046

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

Flipped N/Q/H residues before XYZ refinement:
** B  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 GLN ** 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 = 0.4118 r_free = 0.4118 target = 0.157112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.123546 restraints weight = 10312.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.127697 restraints weight = 6440.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.130502 restraints weight = 4800.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.3784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
moved from start:          0.3213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6349  Z= 0.154
  Angle     :  0.554   9.545   8596  Z= 0.273
  Chirality :  0.040   0.246    942
  Planarity :  0.003   0.031   1047
  Dihedral  :  4.615  58.789    946
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 18.82 %
    Favored  : 77.45 %
  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: -1.05 (0.31), residues: 761
  helix:  0.57 (0.28), residues: 352
  sheet: -1.61 (0.57), residues: 80
  loop : -1.87 (0.36), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 271 
 HIS   0.002   0.000   HIS A 223 
 PHE   0.021   0.001   PHE A 377 
 TYR   0.030   0.001   TYR B 120 
 ARG   0.002   0.000   ARG A 152 

*********************** 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
  134 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 110
  time to evaluate  : 0.639 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.5994 (mmpt) cc_final: 0.5117 (ptmt)
REVERT: A  260 MET cc_start: 0.7630 (tmm) cc_final: 0.7227 (tmm)
REVERT: A  370 MET cc_start: 0.8203 (tpp) cc_final: 0.7971 (tpp)
REVERT: A  464 ARG cc_start: 0.7071 (mmp80) cc_final: 0.4642 (tpp-160)
REVERT: C  110 TYR cc_start: 0.7861 (m-80) cc_final: 0.7530 (m-10)
  outliers start: 24
  outliers final: 19
  residues processed: 128
  average time/residue: 0.1722
  time to fit residues: 29.7824
Evaluate side-chains
  123 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  127 PHE
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  204 TRP
Chi-restraints excluded: chain A residue  263 PHE
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  446 VAL
Chi-restraints excluded: chain A residue  566 PHE
Chi-restraints excluded: chain A residue  604 PHE
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  104 GLU
Chi-restraints excluded: chain C residue  118 VAL
Chi-restraints excluded: chain C residue  126 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 36 optimal weight:    5.9990
   chunk 10 optimal weight:    0.7980
   chunk 56 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 17 optimal weight:    0.7980
   chunk 38 optimal weight:    0.6980
   chunk 53 optimal weight:    5.9990
   chunk 47 optimal weight:    0.5980
   chunk 0 optimal weight:   30.0000
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** B  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 GLN ** 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 = 0.4090 r_free = 0.4090 target = 0.154391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.120112 restraints weight = 10374.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.124207 restraints weight = 6564.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.126581 restraints weight = 4911.039|
|-----------------------------------------------------------------------------|
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.3486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6349  Z= 0.193
  Angle     :  0.571   9.474   8596  Z= 0.283
  Chirality :  0.040   0.242    942
  Planarity :  0.003   0.029   1047
  Dihedral  :  4.741  57.949    946
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 20.37 %
    Favored  : 75.58 %
  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: -0.85 (0.32), residues: 761
  helix:  0.65 (0.28), residues: 352
  sheet: -1.34 (0.55), residues: 98
  loop : -1.69 (0.38), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 204 
 HIS   0.002   0.000   HIS A 223 
 PHE   0.023   0.001   PHE A 377 
 TYR   0.032   0.002   TYR A 358 
 ARG   0.002   0.000   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
  136 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 110
  time to evaluate  : 0.783 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.6022 (mmpt) cc_final: 0.5097 (ptmt)
REVERT: A  260 MET cc_start: 0.7713 (tmm) cc_final: 0.7334 (tmt)
REVERT: A  464 ARG cc_start: 0.7149 (mmp80) cc_final: 0.4792 (tpp-160)
REVERT: A  548 PHE cc_start: 0.7281 (OUTLIER) cc_final: 0.6644 (t80)
REVERT: A  567 GLN cc_start: 0.7557 (mp10) cc_final: 0.7113 (mp10)
REVERT: C   71 LEU cc_start: 0.8601 (tp) cc_final: 0.8325 (tt)
  outliers start: 26
  outliers final: 20
  residues processed: 129
  average time/residue: 0.1952
  time to fit residues: 33.6171
Evaluate side-chains
  129 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 108
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  127 PHE
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  204 TRP
Chi-restraints excluded: chain A residue  263 PHE
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  446 VAL
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  604 PHE
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue  104 GLU
Chi-restraints excluded: chain C residue  118 VAL
Chi-restraints excluded: chain C residue  126 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 68 optimal weight:    4.9990
   chunk 3 optimal weight:    4.9990
   chunk 48 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0870
   chunk 45 optimal weight:    4.9990
   chunk 40 optimal weight:    0.7980
   chunk 64 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 72 optimal weight:    2.9990
   chunk 5 optimal weight:    0.2980
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.6160

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 GLN ** 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 = 0.4093 r_free = 0.4093 target = 0.154598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.121142 restraints weight = 10448.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.125278 restraints weight = 6507.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.128225 restraints weight = 4796.554|
|-----------------------------------------------------------------------------|
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
moved from start:          0.3634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6349  Z= 0.179
  Angle     :  0.591  10.571   8596  Z= 0.289
  Chirality :  0.041   0.240    942
  Planarity :  0.003   0.029   1047
  Dihedral  :  4.731  58.388    946
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 20.84 %
    Favored  : 75.43 %
  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: -0.78 (0.32), residues: 761
  helix:  0.74 (0.28), residues: 352
  sheet: -1.30 (0.58), residues: 87
  loop : -1.70 (0.37), residues: 322

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   0.023   0.001   PHE A 377 
 TYR   0.030   0.002   TYR A 358 
 ARG   0.002   0.000   ARG C  44 

*********************** 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
  136 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 112
  time to evaluate  : 0.677 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.5965 (mmpt) cc_final: 0.5104 (ptmt)
REVERT: A  260 MET cc_start: 0.7708 (tmm) cc_final: 0.7255 (tmm)
REVERT: A  464 ARG cc_start: 0.7142 (mmp80) cc_final: 0.4850 (tpp-160)
REVERT: A  548 PHE cc_start: 0.7098 (OUTLIER) cc_final: 0.6514 (t80)
REVERT: A  567 GLN cc_start: 0.7584 (mp10) cc_final: 0.7216 (mp10)
REVERT: B   53 MET cc_start: 0.7314 (ttt) cc_final: 0.7067 (ttm)
REVERT: C   71 LEU cc_start: 0.8564 (tp) cc_final: 0.8289 (tt)
  outliers start: 24
  outliers final: 21
  residues processed: 128
  average time/residue: 0.2017
  time to fit residues: 34.3447
Evaluate side-chains
  126 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 104
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  127 PHE
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  204 TRP
Chi-restraints excluded: chain A residue  263 PHE
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  446 VAL
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain A residue  566 PHE
Chi-restraints excluded: chain A residue  604 PHE
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   94 TYR
Chi-restraints excluded: chain C residue  104 GLU
Chi-restraints excluded: chain C residue  118 VAL
Chi-restraints excluded: chain C residue  126 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 70 optimal weight:    0.0870
   chunk 37 optimal weight:    7.9990
   chunk 19 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 52 optimal weight:    9.9990
   chunk 11 optimal weight:    0.7980
   chunk 26 optimal weight:    3.9990
   chunk 15 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 456 HIS
** B  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  78 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.150934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.115676 restraints weight = 10247.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.120078 restraints weight = 6123.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.123090 restraints weight = 4420.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7421
moved from start:          0.3812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6349  Z= 0.191
  Angle     :  0.609  10.966   8596  Z= 0.298
  Chirality :  0.041   0.241    942
  Planarity :  0.003   0.029   1047
  Dihedral  :  4.785  57.881    946
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 21.93 %
    Favored  : 73.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.74 (0.32), residues: 761
  helix:  0.77 (0.28), residues: 350
  sheet: -1.18 (0.58), residues: 87
  loop : -1.70 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 204 
 HIS   0.007   0.001   HIS C 100 
 PHE   0.023   0.001   PHE A 586 
 TYR   0.025   0.002   TYR A 358 
 ARG   0.002   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
  137 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 110
  time to evaluate  : 0.610 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.6046 (mmpt) cc_final: 0.5145 (ptmt)
REVERT: A  260 MET cc_start: 0.7697 (tmm) cc_final: 0.7312 (tmt)
REVERT: A  301 THR cc_start: 0.7092 (p) cc_final: 0.6884 (p)
REVERT: A  464 ARG cc_start: 0.7080 (mmp80) cc_final: 0.4796 (tpp-160)
REVERT: A  548 PHE cc_start: 0.7097 (OUTLIER) cc_final: 0.6617 (t80)
REVERT: A  567 GLN cc_start: 0.7652 (mp10) cc_final: 0.7265 (mp10)
REVERT: B   53 MET cc_start: 0.7389 (ttt) cc_final: 0.6964 (ttm)
REVERT: C   71 LEU cc_start: 0.8519 (tp) cc_final: 0.8244 (tt)
REVERT: C   99 ILE cc_start: 0.7379 (pt) cc_final: 0.6504 (tt)
  outliers start: 27
  outliers final: 23
  residues processed: 128
  average time/residue: 0.1815
  time to fit residues: 30.6663
Evaluate side-chains
  131 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 107
  time to evaluate  : 0.636 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  127 PHE
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  204 TRP
Chi-restraints excluded: chain A residue  263 PHE
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  446 VAL
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain A residue  566 PHE
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  604 PHE
Chi-restraints excluded: chain B residue  134 THR
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   94 TYR
Chi-restraints excluded: chain C residue  104 GLU
Chi-restraints excluded: chain C residue  118 VAL
Chi-restraints excluded: chain C residue  126 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 70 optimal weight:    0.0050
   chunk 43 optimal weight:    3.9990
   chunk 66 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 49 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 57 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9990
   overall best weight:    0.6794

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  98 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.153874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.119731 restraints weight = 10400.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.123844 restraints weight = 6501.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.126663 restraints weight = 4826.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
moved from start:          0.3953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6349  Z= 0.195
  Angle     :  0.626  11.439   8596  Z= 0.307
  Chirality :  0.041   0.247    942
  Planarity :  0.004   0.032   1047
  Dihedral  :  4.803  57.712    946
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 21.93 %
    Favored  : 74.03 %
  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: -0.76 (0.31), residues: 761
  helix:  0.79 (0.28), residues: 350
  sheet: -1.26 (0.56), residues: 88
  loop : -1.73 (0.36), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 204 
 HIS   0.006   0.001   HIS C 100 
 PHE   0.027   0.001   PHE A 427 
 TYR   0.024   0.001   TYR B 120 
 ARG   0.009   0.000   ARG C  38 

*********************** 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
  137 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 111
  time to evaluate  : 0.663 
Fit side-chains
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.6017 (mmpt) cc_final: 0.5126 (ptmt)
REVERT: A  260 MET cc_start: 0.7770 (tmm) cc_final: 0.7416 (tmt)
REVERT: A  301 THR cc_start: 0.7075 (p) cc_final: 0.6866 (p)
REVERT: A  464 ARG cc_start: 0.7089 (mmp80) cc_final: 0.4833 (tpp-160)
REVERT: A  548 PHE cc_start: 0.7090 (OUTLIER) cc_final: 0.6672 (t80)
REVERT: A  567 GLN cc_start: 0.7527 (mp10) cc_final: 0.7181 (mp10)
REVERT: B   47 ARG cc_start: 0.7515 (mtm180) cc_final: 0.7211 (mtm-85)
REVERT: B   53 MET cc_start: 0.7338 (ttt) cc_final: 0.7003 (ttm)
REVERT: C   27 SER cc_start: 0.6649 (OUTLIER) cc_final: 0.6096 (m)
REVERT: C   71 LEU cc_start: 0.8544 (tp) cc_final: 0.8283 (tt)
REVERT: C  116 LYS cc_start: 0.5828 (mtmt) cc_final: 0.5300 (ttpt)
  outliers start: 26
  outliers final: 23
  residues processed: 128
  average time/residue: 0.1881
  time to fit residues: 32.1167
Evaluate side-chains
  132 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 107
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  127 PHE
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  204 TRP
Chi-restraints excluded: chain A residue  263 PHE
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  446 VAL
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain A residue  566 PHE
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  604 PHE
Chi-restraints excluded: chain B residue   24 GLN
Chi-restraints excluded: chain B residue   70 ILE
Chi-restraints excluded: chain B residue  134 THR
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   27 SER
Chi-restraints excluded: chain C residue   94 TYR
Chi-restraints excluded: chain C residue  104 GLU
Chi-restraints excluded: chain C residue  126 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 27 optimal weight:    5.9990
   chunk 5 optimal weight:    0.5980
   chunk 73 optimal weight:    4.9990
   chunk 25 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 52 optimal weight:    7.9990
   chunk 41 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  98 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.147994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.116512 restraints weight = 10281.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.120150 restraints weight = 6809.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.122574 restraints weight = 5204.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.4051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6349  Z= 0.205
  Angle     :  0.650  12.021   8596  Z= 0.318
  Chirality :  0.041   0.240    942
  Planarity :  0.004   0.028   1047
  Dihedral  :  4.834  57.633    946
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 22.86 %
    Favored  : 73.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.82 (0.28), residues: 350
  sheet: -1.17 (0.57), residues: 88
  loop : -1.76 (0.36), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 204 
 HIS   0.007   0.001   HIS C 100 
 PHE   0.035   0.001   PHE A 427 
 TYR   0.024   0.001   TYR B 120 
 ARG   0.010   0.000   ARG C  38 

********************** 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
  136 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 110
  time to evaluate  : 0.667 
Fit side-chains
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.5944 (mmpt) cc_final: 0.5094 (ptmt)
REVERT: A  260 MET cc_start: 0.7781 (tmm) cc_final: 0.7440 (tmt)
REVERT: A  301 THR cc_start: 0.7103 (p) cc_final: 0.6893 (p)
REVERT: A  464 ARG cc_start: 0.7104 (mmp80) cc_final: 0.4882 (tpp-160)
REVERT: A  548 PHE cc_start: 0.7121 (OUTLIER) cc_final: 0.6750 (t80)
REVERT: A  567 GLN cc_start: 0.7440 (mp10) cc_final: 0.7126 (mp10)
REVERT: B   47 ARG cc_start: 0.7518 (mtm180) cc_final: 0.7209 (mtm-85)
REVERT: B   53 MET cc_start: 0.7295 (ttt) cc_final: 0.7007 (ttm)
REVERT: C   44 ARG cc_start: 0.7529 (mmm160) cc_final: 0.7276 (mmm160)
REVERT: C   71 LEU cc_start: 0.8571 (tp) cc_final: 0.8299 (tt)
REVERT: C  116 LYS cc_start: 0.5908 (mtmt) cc_final: 0.5212 (ttmt)
  outliers start: 26
  outliers final: 24
  residues processed: 127
  average time/residue: 0.1894
  time to fit residues: 32.4991
Evaluate side-chains
  134 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 109
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  127 PHE
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  204 TRP
Chi-restraints excluded: chain A residue  263 PHE
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  446 VAL
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain A residue  566 PHE
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  604 PHE
Chi-restraints excluded: chain B residue   24 GLN
Chi-restraints excluded: chain B residue   70 ILE
Chi-restraints excluded: chain B residue  134 THR
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   27 SER
Chi-restraints excluded: chain C residue   94 TYR
Chi-restraints excluded: chain C residue  104 GLU
Chi-restraints excluded: chain C residue  126 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 71 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 17 optimal weight:    0.3980
   chunk 27 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   chunk 52 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 GLN ** 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 = 0.3891 r_free = 0.3891 target = 0.147456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.116072 restraints weight = 10316.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.119668 restraints weight = 6861.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.122192 restraints weight = 5252.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.4101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6349  Z= 0.203
  Angle     :  0.652  11.848   8596  Z= 0.318
  Chirality :  0.041   0.258    942
  Planarity :  0.004   0.028   1047
  Dihedral  :  4.830  57.658    946
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 23.64 %
    Favored  : 72.47 %
  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: -0.70 (0.32), residues: 761
  helix:  0.85 (0.28), residues: 347
  sheet: -1.13 (0.57), residues: 88
  loop : -1.74 (0.36), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 204 
 HIS   0.005   0.001   HIS C 100 
 PHE   0.023   0.001   PHE A 377 
 TYR   0.023   0.001   TYR B 120 
 ARG   0.010   0.000   ARG C  38 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2276.48 seconds
wall clock time: 42 minutes 43.43 seconds (2563.43 seconds total)