Starting phenix.real_space_refine
on Wed Sep 17 04:53:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xps_38560/09_2025/8xps_38560.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xps_38560/09_2025/8xps_38560.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.22
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xps_38560/09_2025/8xps_38560.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xps_38560/09_2025/8xps_38560.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xps_38560/09_2025/8xps_38560.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xps_38560/09_2025/8xps_38560.cif"
  }
  resolution = 3.22
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.024 sd=   0.413
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      25      5.16       5
     C    2874      2.51       5
     N     727      2.21       5
     O     942      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4568
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "B"
      Number of atoms: 898
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 898
          Classifications: {'peptide': 119}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 116}
    Chain: "A"
      Number of atoms: 3376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 427, 3376
          Classifications: {'peptide': 427}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 24, 'TRANS': 402}
    Chain: "C"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "D"
      Number of atoms: 72
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 72
          Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
    Chain: "E"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "F"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "G"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
  Time building chain proxies: 1.36, per 1000 atoms: 0.30
  Number of scatterers: 4568
  At special positions: 0
  Unit cell: (84.812, 84.812, 110.908, 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      25     16.00
     O     942      8.00
     N     727      7.00
     C    2874      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 189 " - pdb=" SG  CYS A 601 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 216 " - pdb=" SG  CYS A 240 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 282 " - pdb=" SG  CYS A 295 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 382 " - pdb=" SG  CYS A 395 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 387 " - pdb=" SG  CYS A 499 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 493 " - pdb=" SG  CYS A 503 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 565 " - pdb=" SG  CYS A 574 " 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=0, symmetry=0
  Links applied
    ALPHA1-3
      " BMA D   3 " - " MAN D   6 "
      " BMA G   3 " - " MAN G   4 "
    ALPHA1-6
      " BMA C   3 " - " MAN C   4 "
      " MAN C   4 " - " MAN C   5 "
      " BMA D   3 " - " MAN D   4 "
      " MAN D   4 " - " MAN D   5 "
      " BMA E   3 " - " MAN E   4 "
      " BMA F   3 " - " MAN F   4 "
      " BMA G   3 " - " MAN G   5 "
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " BMA F   3 "
      " NAG G   1 " - " NAG G   2 "
      " NAG G   2 " - " BMA G   3 "
    NAG-ASN
      " NAG C   1 " - " ASN A 417 "
      " NAG D   1 " - " ASN A 306 "
      " NAG E   1 " - " ASN A 195 "
      " NAG F   1 " - " ASN A 529 "
      " NAG G   1 " - " ASN A 378 "
  Time building additional restraints: 0.51
  Conformation dependent library (CDL) restraints added in 128.2 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1010

  Finding SS restraints...
    Secondary structure from input PDB file:
      3 helices and 13 sheets defined
      3.1% alpha, 34.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'B' and resid 87 through 91
      removed outlier: 3.517A  pdb=" N   THR B  91 " --> pdb=" O   ALA B  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 306
    Processing helix  chain 'A' and resid 393 through 399
      removed outlier: 3.590A  pdb=" N   MET A 399 " --> pdb=" O   CYS A 395 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 6
      removed outlier: 3.627A  pdb=" N   GLN B   3 " --> pdb=" O   SER B  25 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 17 through 19
    Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 47
      removed outlier: 3.572A  pdb=" N   SER B  35 " --> pdb=" O   ALA B  97 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 49 through 51
    Processing sheet with id=AA5, first strand: chain 'A' and resid 215 through 225
      removed outlier: 5.994A  pdb=" N   SER A 232 " --> pdb=" O   PRO A 220 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   LEU A 222 " --> pdb=" O   ALA A 230 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   ALA A 230 " --> pdb=" O   LEU A 222 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   MET A 224 " --> pdb=" O   TYR A 228 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   TYR A 228 " --> pdb=" O   MET A 224 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   GLN A 247 " --> pdb=" O   GLU A 235 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 215 through 225
      removed outlier: 5.994A  pdb=" N   SER A 232 " --> pdb=" O   PRO A 220 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   LEU A 222 " --> pdb=" O   ALA A 230 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   ALA A 230 " --> pdb=" O   LEU A 222 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   MET A 224 " --> pdb=" O   TYR A 228 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   TYR A 228 " --> pdb=" O   MET A 224 " (cutoff:3.500A)
      removed outlier: 5.896A  pdb=" N   GLU A 254 " --> pdb=" O   MET A 267 " (cutoff:3.500A)
      removed outlier: 5.051A  pdb=" N   MET A 267 " --> pdb=" O   GLU A 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 279 through 284
      removed outlier: 5.324A  pdb=" N   HIS A 281 " --> pdb=" O   ALA A 296 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   ALA A 296 " --> pdb=" O   HIS A 281 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   LEU A 314 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 350
      removed outlier: 3.836A  pdb=" N   MET A 349 " --> pdb=" O   VAL A 367 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   TYR A 363 " --> pdb=" O   ILE A 356 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ILE A 356 " --> pdb=" O   TYR A 363 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 348 through 350
      removed outlier: 3.836A  pdb=" N   MET A 349 " --> pdb=" O   VAL A 367 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 442 through 447
    Processing sheet with id=AB2, first strand: chain 'A' and resid 468 through 471
      removed outlier: 3.667A  pdb=" N   GLN A 470 " --> pdb=" O   VAL A 476 " (cutoff:3.500A)
      removed outlier: 7.220A  pdb=" N   VAL A 476 " --> pdb=" O   GLN A 470 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 512 through 515
      removed outlier: 6.465A  pdb=" N   ILE A 520 " --> pdb=" O   ILE A 514 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   PHE A 540 " --> pdb=" O   SER A 521 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   TYR A 547 " --> pdb=" O   VAL A 539 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 561 through 567
      removed outlier: 3.532A  pdb=" N   SER A 576 " --> pdb=" O   PHE A 593 " (cutoff:3.500A)

    101 hydrogen bonds defined for protein.
    264 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.66

  Time building geometry restraints manager: 0.63 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 956
        1.33 -     1.45: 1143
        1.45 -     1.57: 2531
        1.57 -     1.69: 3
        1.69 -     1.81: 34
  Bond restraints: 4667
  Sorted by residual:
  bond pdb=" C1  BMA D   3 "
       pdb=" C2  BMA D   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.587 -0.068 2.00e-02 2.50e+03 1.16e+01
  bond pdb=" N   LEU A 475 "
       pdb=" CA  LEU A 475 "
    ideal  model  delta    sigma   weight residual
    1.461  1.500 -0.038 1.30e-02 5.92e+03 8.68e+00
  bond pdb=" N   ASN A 473 "
       pdb=" CA  ASN A 473 "
    ideal  model  delta    sigma   weight residual
    1.462  1.487 -0.026 9.50e-03 1.11e+04 7.35e+00
  bond pdb=" C4  BMA F   3 "
       pdb=" C5  BMA F   3 "
    ideal  model  delta    sigma   weight residual
    1.528  1.582 -0.054 2.00e-02 2.50e+03 7.24e+00
  bond pdb=" N   VAL A 477 "
       pdb=" CA  VAL A 477 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.20e-02 6.94e+03 6.28e+00
  ... (remaining 4662 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.28: 6169
        2.28 -     4.56: 134
        4.56 -     6.84: 37
        6.84 -     9.12: 3
        9.12 -    11.41: 2
  Bond angle restraints: 6345
  Sorted by residual:
  angle pdb=" N   GLN A 470 "
        pdb=" CA  GLN A 470 "
        pdb=" C   GLN A 470 "
      ideal   model   delta    sigma   weight residual
     113.88  105.95    7.93 1.23e+00 6.61e-01 4.16e+01
  angle pdb=" N   PRO A 474 "
        pdb=" CA  PRO A 474 "
        pdb=" C   PRO A 474 "
      ideal   model   delta    sigma   weight residual
     112.47  101.06   11.41 2.06e+00 2.36e-01 3.07e+01
  angle pdb=" CA  ASN A 478 "
        pdb=" C   ASN A 478 "
        pdb=" O   ASN A 478 "
      ideal   model   delta    sigma   weight residual
     120.98  116.51    4.47 1.08e+00 8.57e-01 1.72e+01
  angle pdb=" CA  LEU A 475 "
        pdb=" C   LEU A 475 "
        pdb=" O   LEU A 475 "
      ideal   model   delta    sigma   weight residual
     121.02  116.56    4.46 1.15e+00 7.56e-01 1.50e+01
  angle pdb=" N   PRO A 474 "
        pdb=" CD  PRO A 474 "
        pdb=" CG  PRO A 474 "
      ideal   model   delta    sigma   weight residual
     103.20   98.30    4.90 1.50e+00 4.44e-01 1.07e+01
  ... (remaining 6340 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.21: 2918
       24.21 -    48.41: 88
       48.41 -    72.62: 20
       72.62 -    96.83: 47
       96.83 -   121.03: 25
  Dihedral angle restraints: 3098
    sinusoidal: 1516
      harmonic: 1582
  Sorted by residual:
  dihedral pdb=" C   ASN A 473 "
           pdb=" N   ASN A 473 "
           pdb=" CA  ASN A 473 "
           pdb=" CB  ASN A 473 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.34   11.74     0      2.50e+00 1.60e-01 2.21e+01
  dihedral pdb=" N   ASN A 473 "
           pdb=" C   ASN A 473 "
           pdb=" CA  ASN A 473 "
           pdb=" CB  ASN A 473 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  133.58  -10.78     0      2.50e+00 1.60e-01 1.86e+01
  dihedral pdb=" C2  MAN D   4 "
           pdb=" C1  MAN D   4 "
           pdb=" O5  MAN D   4 "
           pdb=" C5  MAN D   4 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -57.62   63.41 -121.03     1      3.00e+01 1.11e-03 1.62e+01
  ... (remaining 3095 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.087: 684
       0.087 -    0.174: 81
       0.174 -    0.260: 7
       0.260 -    0.347: 2
       0.347 -    0.434: 1
  Chirality restraints: 775
  Sorted by residual:
  chirality pdb=" CA  ASN A 473 "
            pdb=" N   ASN A 473 "
            pdb=" C   ASN A 473 "
            pdb=" CB  ASN A 473 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.71e+00
  chirality pdb=" CA  VAL A 477 "
            pdb=" N   VAL A 477 "
            pdb=" C   VAL A 477 "
            pdb=" CB  VAL A 477 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.75   -0.30 2.00e-01 2.50e+01 2.32e+00
  chirality pdb=" C5  BMA G   3 "
            pdb=" C4  BMA G   3 "
            pdb=" C6  BMA G   3 "
            pdb=" O5  BMA G   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.54    0.26 2.00e-01 2.50e+01 1.71e+00
  ... (remaining 772 not shown)

  Planarity restraints: 783
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 473 "    0.014 2.00e-02 2.50e+03   2.71e-02 7.37e+00
        pdb=" C   ASN A 473 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   ASN A 473 "    0.017 2.00e-02 2.50e+03
        pdb=" N   PRO A 474 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 467 "    0.010 2.00e-02 2.50e+03   2.05e-02 4.21e+00
        pdb=" C   GLY A 467 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   GLY A 467 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ASP A 468 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 473 "    0.026 5.00e-02 4.00e+02   3.92e-02 2.46e+00
        pdb=" N   PRO A 474 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 474 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 474 "    0.022 5.00e-02 4.00e+02
  ... (remaining 780 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 418
        2.75 -     3.28: 4268
        3.28 -     3.82: 7226
        3.82 -     4.36: 8373
        4.36 -     4.90: 14560
  Nonbonded interactions: 34845
  Sorted by model distance:
  nonbonded pdb=" O3  NAG G   2 "
            pdb=" O2  BMA G   3 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" OH  TYR B  32 "
            pdb=" O   ASP A 257 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" OH  TYR A 454 "
            pdb=" O   ASN A 509 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" O3  NAG F   2 "
            pdb=" O2  BMA F   3 "
     model   vdw
     2.334 3.040
  nonbonded pdb=" O3  NAG D   2 "
            pdb=" O2  BMA D   3 "
     model   vdw
     2.348 3.040
  ... (remaining 34840 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
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.960
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.130
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
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      :  0.005   0.068   4699  Z= 0.274
  Angle     :  0.872  11.406   6433  Z= 0.432
  Chirality :  0.057   0.434    775
  Planarity :  0.003   0.039    778
  Dihedral  : 20.478 121.032   2064
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  :  9.04 %
    Favored  : 90.59 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  :  5.62 %
    Favored  : 89.79 %
  Cbeta Deviations :  0.20 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.49 (0.29), residues: 542
  helix: -1.38 (2.33), residues: 6
  sheet: -2.13 (0.35), residues: 173
  loop : -3.70 (0.25), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  98 
 TYR   0.004   0.001   TYR A 454 
 PHE   0.005   0.001   PHE A 537 
 TRP   0.004   0.001   TRP A 310 
 HIS   0.001   0.000   HIS A 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00494 ( 4667)
  covalent geometry    : angle       0.85211 ( 6345)
  SS BOND              : bond        0.00096 (    8)
  SS BOND              : angle       0.54201 (   16)
  hydrogen bonds       : bond        0.30114 (   96)
  hydrogen bonds       : angle      10.72727 (  264)
  link_ALPHA1-3        : bond        0.00454 (    2)
  link_ALPHA1-3        : angle       1.61709 (    6)
  link_ALPHA1-6        : bond        0.00709 (    7)
  link_ALPHA1-6        : angle       1.43491 (   21)
  link_BETA1-4         : bond        0.01105 (   10)
  link_BETA1-4         : angle       2.36185 (   30)
  link_NAG-ASN         : bond        0.00151 (    5)
  link_NAG-ASN         : angle       1.87321 (   15)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 135
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   20 LEU cc_start: 0.8858 (mt) cc_final: 0.8344 (mt)
REVERT: A  197 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8311 (tp)
REVERT: A  360 ASP cc_start: 0.7905 (t0) cc_final: 0.7690 (t0)
  outliers start: 22
  outliers final: 4
  residues processed: 147
  average time/residue: 0.0909
  time to fit residues: 16.2409
Evaluate side-chains
  102 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 97
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 ARG
Chi-restraints excluded: chain B residue   96 CYS
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  389 TYR
Chi-restraints excluded: chain A residue  472 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 50 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0670
   chunk 30 optimal weight:    4.9990
   overall best weight:    0.7720

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

Flipped N/Q/H residues before XYZ refinement:
** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 247 GLN
A 326 ASN
A 334 GLN
A 358 GLN
A 394 ASN
A 478 ASN
A 534 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.063099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.056065 restraints weight = 15557.539|
|-----------------------------------------------------------------------------|
r_work (start): 0.3071 rms_B_bonded: 2.96
r_work: 0.2962 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          0.2922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   4699  Z= 0.180
  Angle     :  0.860  12.982   6433  Z= 0.388
  Chirality :  0.049   0.206    775
  Planarity :  0.005   0.042    778
  Dihedral  : 21.166 108.794   1082
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.86 %
    Favored  : 91.14 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 12.50 %
    Favored  : 82.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.81 (0.31), residues: 542
  helix: -3.41 (0.79), residues: 6
  sheet: -1.54 (0.38), residues: 175
  loop : -3.25 (0.27), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 402 
 TYR   0.020   0.002   TYR B  50 
 PHE   0.017   0.002   PHE A 364 
 TRP   0.010   0.001   TRP A 573 
 HIS   0.001   0.000   HIS A 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 4667)
  covalent geometry    : angle       0.79907 ( 6345)
  SS BOND              : bond        0.00564 (    8)
  SS BOND              : angle       1.41284 (   16)
  hydrogen bonds       : bond        0.03970 (   96)
  hydrogen bonds       : angle       6.39909 (  264)
  link_ALPHA1-3        : bond        0.00958 (    2)
  link_ALPHA1-3        : angle       2.08277 (    6)
  link_ALPHA1-6        : bond        0.01466 (    7)
  link_ALPHA1-6        : angle       2.92461 (   21)
  link_BETA1-4         : bond        0.01307 (   10)
  link_BETA1-4         : angle       2.83818 (   30)
  link_NAG-ASN         : bond        0.01310 (    5)
  link_NAG-ASN         : angle       3.90789 (   15)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 102
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   73 ASP cc_start: 0.7927 (t0) cc_final: 0.7583 (t0)
REVERT: B   76 LYS cc_start: 0.8469 (mmtt) cc_final: 0.8091 (mmtt)
REVERT: B  103 VAL cc_start: 0.7997 (m) cc_final: 0.7591 (m)
REVERT: A  291 TYR cc_start: 0.8916 (OUTLIER) cc_final: 0.8210 (t80)
REVERT: A  360 ASP cc_start: 0.8479 (t0) cc_final: 0.8139 (t0)
REVERT: A  470 GLN cc_start: 0.8336 (pt0) cc_final: 0.8115 (pt0)
  outliers start: 25
  outliers final: 12
  residues processed: 117
  average time/residue: 0.0778
  time to fit residues: 11.4790
Evaluate side-chains
  105 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  116 THR
Chi-restraints excluded: chain A residue  216 CYS
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  389 TYR
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  477 VAL
Chi-restraints excluded: chain A residue  519 TRP
Chi-restraints excluded: chain A residue  553 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0980
   chunk 26 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 31 optimal weight:    0.2980
   chunk 27 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 48 optimal weight:    0.7980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 394 ASN
A 534 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.059308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.052277 restraints weight = 15683.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.2970 rms_B_bonded: 2.96
r_work: 0.2864 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8576
moved from start:          0.3716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4699  Z= 0.192
  Angle     :  0.848  10.663   6433  Z= 0.385
  Chirality :  0.049   0.255    775
  Planarity :  0.004   0.034    778
  Dihedral  : 19.180 106.488   1074
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.04 %
    Favored  : 90.96 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 15.62 %
    Favored  : 79.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.29 (0.32), residues: 542
  helix: -1.75 (1.35), residues: 6
  sheet: -0.99 (0.38), residues: 176
  loop : -3.04 (0.28), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 242 
 TYR   0.015   0.002   TYR A 351 
 PHE   0.020   0.002   PHE A 537 
 TRP   0.012   0.001   TRP B 104 
 HIS   0.002   0.001   HIS A 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 4667)
  covalent geometry    : angle       0.79112 ( 6345)
  SS BOND              : bond        0.00258 (    8)
  SS BOND              : angle       1.67260 (   16)
  hydrogen bonds       : bond        0.03740 (   96)
  hydrogen bonds       : angle       5.60084 (  264)
  link_ALPHA1-3        : bond        0.01141 (    2)
  link_ALPHA1-3        : angle       1.70035 (    6)
  link_ALPHA1-6        : bond        0.01582 (    7)
  link_ALPHA1-6        : angle       2.95265 (   21)
  link_BETA1-4         : bond        0.01188 (   10)
  link_BETA1-4         : angle       2.53425 (   30)
  link_NAG-ASN         : bond        0.01166 (    5)
  link_NAG-ASN         : angle       3.75626 (   15)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
REVERT: B   73 ASP cc_start: 0.7953 (t0) cc_final: 0.7623 (t0)
REVERT: B   76 LYS cc_start: 0.8472 (mmtt) cc_final: 0.8152 (mmtt)
REVERT: B  117 VAL cc_start: 0.9149 (t) cc_final: 0.8872 (m)
REVERT: A  261 GLU cc_start: 0.8472 (tp30) cc_final: 0.8141 (tp30)
REVERT: A  291 TYR cc_start: 0.8955 (OUTLIER) cc_final: 0.8263 (t80)
REVERT: A  326 ASN cc_start: 0.8378 (p0) cc_final: 0.7925 (p0)
REVERT: A  360 ASP cc_start: 0.8483 (t0) cc_final: 0.8133 (t0)
REVERT: A  394 ASN cc_start: 0.8773 (m110) cc_final: 0.8567 (m-40)
REVERT: A  450 GLN cc_start: 0.8052 (tt0) cc_final: 0.7832 (tt0)
REVERT: A  466 PHE cc_start: 0.8273 (m-80) cc_final: 0.7819 (m-10)
REVERT: A  534 ASN cc_start: 0.8929 (OUTLIER) cc_final: 0.7619 (t0)
REVERT: A  569 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8312 (pttm)
  outliers start: 22
  outliers final: 10
  residues processed: 108
  average time/residue: 0.0797
  time to fit residues: 10.7104
Evaluate side-chains
  99 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   39 GLN
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  519 TRP
Chi-restraints excluded: chain A residue  534 ASN
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  569 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0170
   chunk 38 optimal weight:    0.5980
   chunk 41 optimal weight:    0.0980
   chunk 31 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 7 optimal weight:    0.6980
   chunk 10 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.4820

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

Flipped N/Q/H residues before XYZ refinement:
B   3 GLN
A 388 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.059777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.052682 restraints weight = 15747.197|
|-----------------------------------------------------------------------------|
r_work (start): 0.2986 rms_B_bonded: 2.95
r_work: 0.2875 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start:          0.4068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4699  Z= 0.150
  Angle     :  0.838  13.358   6433  Z= 0.372
  Chirality :  0.048   0.273    775
  Planarity :  0.004   0.032    778
  Dihedral  : 17.562 107.570   1072
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.56 %
    Favored  : 92.44 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 14.79 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.91 (0.33), residues: 542
  helix: -0.75 (1.56), residues: 6
  sheet: -0.56 (0.39), residues: 177
  loop : -2.89 (0.28), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 242 
 TYR   0.012   0.001   TYR A 351 
 PHE   0.012   0.002   PHE A 537 
 TRP   0.012   0.001   TRP B 104 
 HIS   0.006   0.001   HIS A 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 4667)
  covalent geometry    : angle       0.78581 ( 6345)
  SS BOND              : bond        0.00291 (    8)
  SS BOND              : angle       1.29238 (   16)
  hydrogen bonds       : bond        0.03237 (   96)
  hydrogen bonds       : angle       5.27760 (  264)
  link_ALPHA1-3        : bond        0.01211 (    2)
  link_ALPHA1-3        : angle       1.75215 (    6)
  link_ALPHA1-6        : bond        0.01771 (    7)
  link_ALPHA1-6        : angle       3.07322 (   21)
  link_BETA1-4         : bond        0.01165 (   10)
  link_BETA1-4         : angle       2.51213 (   30)
  link_NAG-ASN         : bond        0.00639 (    5)
  link_NAG-ASN         : angle       3.37531 (   15)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 88
  time to evaluate  : 0.176 
Fit side-chains
REVERT: B   73 ASP cc_start: 0.7925 (t0) cc_final: 0.7591 (t0)
REVERT: B   76 LYS cc_start: 0.8541 (mmtt) cc_final: 0.8238 (mmtt)
REVERT: A  199 LYS cc_start: 0.9163 (mmmm) cc_final: 0.8955 (mmmm)
REVERT: A  291 TYR cc_start: 0.8946 (OUTLIER) cc_final: 0.8238 (t80)
REVERT: A  360 ASP cc_start: 0.8491 (t0) cc_final: 0.8147 (t0)
REVERT: A  466 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.7703 (m-10)
  outliers start: 25
  outliers final: 13
  residues processed: 104
  average time/residue: 0.0736
  time to fit residues: 9.7662
Evaluate side-chains
  97 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 82
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    3 GLN
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   39 GLN
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  116 THR
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  466 PHE
Chi-restraints excluded: chain A residue  519 TRP
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  555 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 247 GLN
A 332 GLN
** A 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 394 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.056025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.048901 restraints weight = 15798.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.2882 rms_B_bonded: 3.00
r_work: 0.2771 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.2771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8660
moved from start:          0.4577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065   4699  Z= 0.247
  Angle     :  0.903  10.006   6433  Z= 0.412
  Chirality :  0.050   0.277    775
  Planarity :  0.005   0.040    778
  Dihedral  : 16.943 107.873   1072
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.96 %
    Favored  : 90.04 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 15.83 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.73 (0.33), residues: 542
  helix:  0.70 (2.22), residues: 6
  sheet: -0.35 (0.39), residues: 176
  loop : -2.84 (0.28), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 402 
 TYR   0.018   0.002   TYR A 351 
 PHE   0.019   0.003   PHE B  68 
 TRP   0.010   0.002   TRP B 104 
 HIS   0.008   0.002   HIS A 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00560 ( 4667)
  covalent geometry    : angle       0.84702 ( 6345)
  SS BOND              : bond        0.00774 (    8)
  SS BOND              : angle       1.53554 (   16)
  hydrogen bonds       : bond        0.03601 (   96)
  hydrogen bonds       : angle       5.37798 (  264)
  link_ALPHA1-3        : bond        0.01043 (    2)
  link_ALPHA1-3        : angle       1.98309 (    6)
  link_ALPHA1-6        : bond        0.01543 (    7)
  link_ALPHA1-6        : angle       3.15169 (   21)
  link_BETA1-4         : bond        0.01131 (   10)
  link_BETA1-4         : angle       2.66531 (   30)
  link_NAG-ASN         : bond        0.00645 (    5)
  link_NAG-ASN         : angle       3.69664 (   15)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 86
  time to evaluate  : 0.147 
Fit side-chains
REVERT: B   73 ASP cc_start: 0.7998 (t0) cc_final: 0.7515 (t0)
REVERT: B   76 LYS cc_start: 0.8533 (mmtt) cc_final: 0.8185 (mmtt)
REVERT: A  199 LYS cc_start: 0.9201 (mmmm) cc_final: 0.8992 (mmmm)
REVERT: A  261 GLU cc_start: 0.8573 (tp30) cc_final: 0.8221 (tp30)
REVERT: A  291 TYR cc_start: 0.9024 (OUTLIER) cc_final: 0.8246 (t80)
REVERT: A  360 ASP cc_start: 0.8593 (t0) cc_final: 0.8200 (t0)
REVERT: A  394 ASN cc_start: 0.8754 (m110) cc_final: 0.8548 (m-40)
REVERT: A  466 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7979 (m-10)
REVERT: A  569 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8410 (pttm)
  outliers start: 20
  outliers final: 10
  residues processed: 97
  average time/residue: 0.0715
  time to fit residues: 8.8176
Evaluate side-chains
  96 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    3 GLN
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  116 THR
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  466 PHE
Chi-restraints excluded: chain A residue  519 TRP
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  569 LYS
Chi-restraints excluded: chain A residue  600 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 32 optimal weight:    0.0000
   chunk 38 optimal weight:    0.0070
   chunk 8 optimal weight:    2.9990
   chunk 4 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9990
   chunk 14 optimal weight:    0.3980
   chunk 40 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 19 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.3602

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

Flipped N/Q/H residues before XYZ refinement:
B   3 GLN
** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 247 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.058799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.051597 restraints weight = 15593.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.2956 rms_B_bonded: 2.98
r_work: 0.2846 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.2846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8605
moved from start:          0.4736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4699  Z= 0.149
  Angle     :  0.849   9.140   6433  Z= 0.387
  Chirality :  0.049   0.280    775
  Planarity :  0.004   0.038    778
  Dihedral  : 16.069 110.094   1072
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.23 %
    Favored  : 90.77 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 16.04 %
    Favored  : 79.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.52 (0.34), residues: 542
  helix:  0.80 (2.10), residues: 6
  sheet: -0.23 (0.39), residues: 181
  loop : -2.71 (0.29), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 242 
 TYR   0.013   0.001   TYR A 280 
 PHE   0.019   0.002   PHE B  68 
 TRP   0.012   0.001   TRP B  47 
 HIS   0.006   0.001   HIS A 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 4667)
  covalent geometry    : angle       0.79612 ( 6345)
  SS BOND              : bond        0.00279 (    8)
  SS BOND              : angle       1.90349 (   16)
  hydrogen bonds       : bond        0.02949 (   96)
  hydrogen bonds       : angle       5.20063 (  264)
  link_ALPHA1-3        : bond        0.01261 (    2)
  link_ALPHA1-3        : angle       1.64839 (    6)
  link_ALPHA1-6        : bond        0.01669 (    7)
  link_ALPHA1-6        : angle       3.07143 (   21)
  link_BETA1-4         : bond        0.01193 (   10)
  link_BETA1-4         : angle       2.51184 (   30)
  link_NAG-ASN         : bond        0.00506 (    5)
  link_NAG-ASN         : angle       3.19288 (   15)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 85
  time to evaluate  : 0.226 
Fit side-chains
REVERT: B   73 ASP cc_start: 0.7959 (t0) cc_final: 0.7678 (t0)
REVERT: B   76 LYS cc_start: 0.8552 (mmtt) cc_final: 0.8326 (mmtt)
REVERT: A  261 GLU cc_start: 0.8543 (tp30) cc_final: 0.8331 (tp30)
REVERT: A  291 TYR cc_start: 0.8988 (OUTLIER) cc_final: 0.8179 (t80)
REVERT: A  360 ASP cc_start: 0.8474 (t0) cc_final: 0.8086 (t0)
REVERT: A  394 ASN cc_start: 0.8693 (m110) cc_final: 0.8449 (m-40)
REVERT: A  466 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7856 (m-10)
  outliers start: 20
  outliers final: 11
  residues processed: 97
  average time/residue: 0.0796
  time to fit residues: 9.7114
Evaluate side-chains
  96 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   18 LEU
Chi-restraints excluded: chain B residue   39 GLN
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  466 PHE
Chi-restraints excluded: chain A residue  519 TRP
Chi-restraints excluded: chain A residue  553 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 4 optimal weight:    7.9990
   chunk 23 optimal weight:    0.9980
   chunk 49 optimal weight:    5.9990
   chunk 0 optimal weight:    4.9990
   chunk 28 optimal weight:    0.5980
   chunk 24 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 247 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.057395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.050200 restraints weight = 15473.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.2916 rms_B_bonded: 2.97
r_work: 0.2806 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8638
moved from start:          0.4912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   4699  Z= 0.175
  Angle     :  0.866   9.029   6433  Z= 0.393
  Chirality :  0.049   0.273    775
  Planarity :  0.005   0.036    778
  Dihedral  : 15.047 109.250   1072
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.86 %
    Favored  : 91.14 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 17.08 %
    Favored  : 79.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.31 (0.34), residues: 542
  helix:  1.34 (2.23), residues: 6
  sheet: -0.10 (0.39), residues: 183
  loop : -2.57 (0.30), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  67 
 TYR   0.014   0.001   TYR B  80 
 PHE   0.021   0.002   PHE B  68 
 TRP   0.008   0.001   TRP B  47 
 HIS   0.006   0.001   HIS A 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 4667)
  covalent geometry    : angle       0.81649 ( 6345)
  SS BOND              : bond        0.00316 (    8)
  SS BOND              : angle       1.73347 (   16)
  hydrogen bonds       : bond        0.02988 (   96)
  hydrogen bonds       : angle       5.08694 (  264)
  link_ALPHA1-3        : bond        0.01172 (    2)
  link_ALPHA1-3        : angle       1.76629 (    6)
  link_ALPHA1-6        : bond        0.01629 (    7)
  link_ALPHA1-6        : angle       2.91882 (   21)
  link_BETA1-4         : bond        0.01149 (   10)
  link_BETA1-4         : angle       2.56918 (   30)
  link_NAG-ASN         : bond        0.00430 (    5)
  link_NAG-ASN         : angle       3.16495 (   15)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
REVERT: B   73 ASP cc_start: 0.8008 (t0) cc_final: 0.7592 (t0)
REVERT: B   76 LYS cc_start: 0.8564 (mmtt) cc_final: 0.8286 (mmtt)
REVERT: B   78 THR cc_start: 0.8939 (p) cc_final: 0.8677 (p)
REVERT: A  261 GLU cc_start: 0.8531 (tp30) cc_final: 0.8322 (tp30)
REVERT: A  291 TYR cc_start: 0.9005 (OUTLIER) cc_final: 0.8186 (t80)
REVERT: A  360 ASP cc_start: 0.8514 (t0) cc_final: 0.8106 (t0)
REVERT: A  394 ASN cc_start: 0.8707 (m110) cc_final: 0.8471 (m-40)
REVERT: A  466 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7874 (m-10)
  outliers start: 17
  outliers final: 14
  residues processed: 91
  average time/residue: 0.0751
  time to fit residues: 8.6736
Evaluate side-chains
  93 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   39 GLN
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   68 PHE
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  466 PHE
Chi-restraints excluded: chain A residue  519 TRP
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  600 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 23 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 5 optimal weight:    0.2980
   chunk 13 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 29 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 38 optimal weight:    0.1980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A 233 HIS ** 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 = 0.3109 r_free = 0.3109 target = 0.057219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.049952 restraints weight = 15925.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.2911 rms_B_bonded: 3.03
r_work: 0.2800 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8644
moved from start:          0.5050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4699  Z= 0.172
  Angle     :  0.856   9.521   6433  Z= 0.393
  Chirality :  0.049   0.271    775
  Planarity :  0.004   0.035    778
  Dihedral  : 14.419 110.183   1072
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.86 %
    Favored  : 91.14 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 16.88 %
    Favored  : 79.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.21 (0.35), residues: 542
  helix:  1.43 (2.24), residues: 6
  sheet:  0.00 (0.40), residues: 177
  loop : -2.48 (0.30), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 242 
 TYR   0.013   0.001   TYR A 351 
 PHE   0.020   0.002   PHE B  68 
 TRP   0.008   0.001   TRP B  47 
 HIS   0.005   0.001   HIS A 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 4667)
  covalent geometry    : angle       0.81111 ( 6345)
  SS BOND              : bond        0.00470 (    8)
  SS BOND              : angle       1.30711 (   16)
  hydrogen bonds       : bond        0.02913 (   96)
  hydrogen bonds       : angle       5.04290 (  264)
  link_ALPHA1-3        : bond        0.01151 (    2)
  link_ALPHA1-3        : angle       1.69800 (    6)
  link_ALPHA1-6        : bond        0.01519 (    7)
  link_ALPHA1-6        : angle       2.66548 (   21)
  link_BETA1-4         : bond        0.01130 (   10)
  link_BETA1-4         : angle       2.56036 (   30)
  link_NAG-ASN         : bond        0.00412 (    5)
  link_NAG-ASN         : angle       3.17622 (   15)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 83
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
REVERT: B   73 ASP cc_start: 0.8044 (t0) cc_final: 0.7631 (t0)
REVERT: B   76 LYS cc_start: 0.8611 (mmtt) cc_final: 0.8350 (mmtt)
REVERT: B   78 THR cc_start: 0.8965 (p) cc_final: 0.8661 (p)
REVERT: B  117 VAL cc_start: 0.9097 (t) cc_final: 0.8880 (m)
REVERT: A  291 TYR cc_start: 0.9020 (OUTLIER) cc_final: 0.8135 (t80)
REVERT: A  360 ASP cc_start: 0.8455 (t0) cc_final: 0.7989 (t0)
REVERT: A  394 ASN cc_start: 0.8734 (m110) cc_final: 0.8505 (m-40)
REVERT: A  466 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.7884 (m-10)
REVERT: A  569 LYS cc_start: 0.8592 (pttp) cc_final: 0.8386 (pttp)
  outliers start: 18
  outliers final: 11
  residues processed: 95
  average time/residue: 0.0785
  time to fit residues: 9.4490
Evaluate side-chains
  95 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  466 PHE
Chi-restraints excluded: chain A residue  519 TRP
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  553 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 25 optimal weight:    0.2980
   chunk 13 optimal weight:    0.8980
   chunk 37 optimal weight:    0.8980
   chunk 19 optimal weight:    0.3980
   chunk 30 optimal weight:    0.0470
   chunk 52 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0870
   chunk 29 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.3056

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

Flipped N/Q/H residues before XYZ refinement:
** A 233 HIS ** 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 = 0.3150 r_free = 0.3150 target = 0.058839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.051538 restraints weight = 15457.394|
|-----------------------------------------------------------------------------|
r_work (start): 0.2953 rms_B_bonded: 3.02
r_work: 0.2842 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8606
moved from start:          0.5082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4699  Z= 0.147
  Angle     :  0.842  10.194   6433  Z= 0.390
  Chirality :  0.048   0.263    775
  Planarity :  0.004   0.040    778
  Dihedral  : 13.971 110.313   1072
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.12 %
    Favored  : 91.88 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 18.54 %
    Favored  : 78.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.09 (0.35), residues: 542
  helix:  1.36 (2.21), residues: 6
  sheet:  0.03 (0.39), residues: 186
  loop : -2.42 (0.31), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 242 
 TYR   0.012   0.001   TYR A 280 
 PHE   0.018   0.001   PHE B  68 
 TRP   0.009   0.001   TRP B  47 
 HIS   0.004   0.001   HIS A 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 4667)
  covalent geometry    : angle       0.79968 ( 6345)
  SS BOND              : bond        0.00342 (    8)
  SS BOND              : angle       1.10757 (   16)
  hydrogen bonds       : bond        0.02756 (   96)
  hydrogen bonds       : angle       4.89671 (  264)
  link_ALPHA1-3        : bond        0.01136 (    2)
  link_ALPHA1-3        : angle       1.59382 (    6)
  link_ALPHA1-6        : bond        0.01516 (    7)
  link_ALPHA1-6        : angle       2.53234 (   21)
  link_BETA1-4         : bond        0.01173 (   10)
  link_BETA1-4         : angle       2.59366 (   30)
  link_NAG-ASN         : bond        0.00353 (    5)
  link_NAG-ASN         : angle       2.91258 (   15)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 82
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
REVERT: B   73 ASP cc_start: 0.8000 (t0) cc_final: 0.7599 (t0)
REVERT: B   78 THR cc_start: 0.8873 (p) cc_final: 0.8620 (p)
REVERT: A  291 TYR cc_start: 0.8989 (OUTLIER) cc_final: 0.8143 (t80)
REVERT: A  360 ASP cc_start: 0.8504 (t0) cc_final: 0.8022 (t0)
REVERT: A  394 ASN cc_start: 0.8725 (m110) cc_final: 0.8464 (m-40)
REVERT: A  466 PHE cc_start: 0.8125 (OUTLIER) cc_final: 0.7786 (m-10)
  outliers start: 15
  outliers final: 9
  residues processed: 92
  average time/residue: 0.0791
  time to fit residues: 9.2225
Evaluate side-chains
  91 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  466 PHE
Chi-restraints excluded: chain A residue  519 TRP
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  553 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 1 optimal weight:    0.1980
   chunk 20 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 17 optimal weight:    0.0570
   chunk 5 optimal weight:    0.0050
   chunk 52 optimal weight:    1.9990
   chunk 6 optimal weight:    0.1980
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.2712

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

Flipped N/Q/H residues before XYZ refinement:
** A 233 HIS ** 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 = 0.3163 r_free = 0.3163 target = 0.059527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.052221 restraints weight = 15384.389|
|-----------------------------------------------------------------------------|
r_work (start): 0.2975 rms_B_bonded: 3.03
r_work: 0.2864 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8588
moved from start:          0.5131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4699  Z= 0.145
  Angle     :  0.839  10.012   6433  Z= 0.388
  Chirality :  0.047   0.254    775
  Planarity :  0.004   0.043    778
  Dihedral  : 13.570 109.516   1072
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.86 %
    Favored  : 91.14 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 19.38 %
    Favored  : 77.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.99 (0.35), residues: 542
  helix:  1.42 (2.21), residues: 6
  sheet:  0.12 (0.40), residues: 183
  loop : -2.34 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 242 
 TYR   0.012   0.001   TYR A 280 
 PHE   0.019   0.001   PHE B  68 
 TRP   0.008   0.001   TRP B  47 
 HIS   0.003   0.001   HIS A 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 4667)
  covalent geometry    : angle       0.79944 ( 6345)
  SS BOND              : bond        0.00196 (    8)
  SS BOND              : angle       1.04687 (   16)
  hydrogen bonds       : bond        0.02669 (   96)
  hydrogen bonds       : angle       4.78974 (  264)
  link_ALPHA1-3        : bond        0.01095 (    2)
  link_ALPHA1-3        : angle       1.53427 (    6)
  link_ALPHA1-6        : bond        0.01511 (    7)
  link_ALPHA1-6        : angle       2.49414 (   21)
  link_BETA1-4         : bond        0.01176 (   10)
  link_BETA1-4         : angle       2.58297 (   30)
  link_NAG-ASN         : bond        0.00317 (    5)
  link_NAG-ASN         : angle       2.74006 (   15)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
REVERT: B   73 ASP cc_start: 0.8108 (t0) cc_final: 0.7722 (t0)
REVERT: B   78 THR cc_start: 0.8885 (p) cc_final: 0.8616 (p)
REVERT: A  235 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8118 (mp0)
REVERT: A  291 TYR cc_start: 0.8955 (OUTLIER) cc_final: 0.8027 (t80)
REVERT: A  360 ASP cc_start: 0.8430 (t0) cc_final: 0.7931 (t0)
REVERT: A  394 ASN cc_start: 0.8724 (m110) cc_final: 0.8436 (m-40)
REVERT: A  466 PHE cc_start: 0.8030 (OUTLIER) cc_final: 0.7728 (m-10)
  outliers start: 14
  outliers final: 11
  residues processed: 90
  average time/residue: 0.0806
  time to fit residues: 9.2031
Evaluate side-chains
  92 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 79
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   39 GLN
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue  107 ASP
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  241 SER
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  466 PHE
Chi-restraints excluded: chain A residue  519 TRP
Chi-restraints excluded: chain A residue  538 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 26 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 233 HIS ** 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 = 0.3121 r_free = 0.3121 target = 0.057806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.050569 restraints weight = 15418.046|
|-----------------------------------------------------------------------------|
r_work (start): 0.2924 rms_B_bonded: 3.01
r_work: 0.2813 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8631
moved from start:          0.5243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4699  Z= 0.171
  Angle     :  0.865   9.909   6433  Z= 0.399
  Chirality :  0.048   0.251    775
  Planarity :  0.004   0.040    778
  Dihedral  : 13.350 108.607   1072
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.67 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 19.79 %
    Favored  : 77.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.92 (0.36), residues: 542
  helix:  1.74 (2.29), residues: 6
  sheet:  0.12 (0.39), residues: 185
  loop : -2.28 (0.31), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 242 
 TYR   0.012   0.001   TYR A 351 
 PHE   0.022   0.002   PHE B  68 
 TRP   0.010   0.001   TRP B  47 
 HIS   0.004   0.001   HIS A 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 4667)
  covalent geometry    : angle       0.82375 ( 6345)
  SS BOND              : bond        0.00189 (    8)
  SS BOND              : angle       1.16126 (   16)
  hydrogen bonds       : bond        0.02822 (   96)
  hydrogen bonds       : angle       4.84595 (  264)
  link_ALPHA1-3        : bond        0.01002 (    2)
  link_ALPHA1-3        : angle       1.63382 (    6)
  link_ALPHA1-6        : bond        0.01456 (    7)
  link_ALPHA1-6        : angle       2.50025 (   21)
  link_BETA1-4         : bond        0.01147 (   10)
  link_BETA1-4         : angle       2.63432 (   30)
  link_NAG-ASN         : bond        0.00398 (    5)
  link_NAG-ASN         : angle       2.95307 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1102.73 seconds
wall clock time: 19 minutes 39.88 seconds (1179.88 seconds total)