Starting phenix.real_space_refine
on Fri Aug 22 22:10:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j74_36025/08_2025/8j74_36025.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j74_36025/08_2025/8j74_36025.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j74_36025/08_2025/8j74_36025.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j74_36025/08_2025/8j74_36025.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j74_36025/08_2025/8j74_36025.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j74_36025/08_2025/8j74_36025.cif"
  }
  resolution = 3.6
  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=   0.004 sd=   0.061
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      40      5.16       5
     C    5546      2.51       5
     N    1214      2.21       5
     O    1488      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8288
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3959
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 515, 3959
          Classifications: {'peptide': 515}
          Link IDs: {'PTRANS': 22, 'TRANS': 492}
    Chain: "E"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 146
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 146
          Unusual residues: {'AV0': 1, 'HC6': 1, 'R16': 1, 'Y01': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 116
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 116
          Unusual residues: {'AV0': 1, 'R16': 1, 'Y01': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
  Restraints were copied for chains:
    B, F
  Time building chain proxies: 2.05, per 1000 atoms: 0.25
  Number of scatterers: 8288
  At special positions: 0
  Unit cell: (100.86, 100.86, 95.94, 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      40     16.00
     O    1488      8.00
     N    1214      7.00
     C    5546      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " BMA F   3 "
    NAG-ASN
      " NAG E   1 " - " ASN A 301 "
      " NAG F   1 " - " ASN B 301 "
  Time building additional restraints: 0.70
  Conformation dependent library (CDL) restraints added in 285.0 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1872

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 2 sheets defined
      77.5% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 29
      removed outlier: 3.548A  pdb=" N   LEU A   8 " --> pdb=" O   HIS A   4 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 45
    Processing helix  chain 'A' and resid 46 through 48
      No H-bonds generated for 'chain 'A' and resid 46 through 48'
    Processing helix  chain 'A' and resid 50 through 63
      removed outlier: 3.529A  pdb=" N   VAL A  63 " --> pdb=" O   THR A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 77
      removed outlier: 3.815A  pdb=" N   THR A  71 " --> pdb=" O   TYR A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 102
    Processing helix  chain 'A' and resid 103 through 109
      removed outlier: 3.645A  pdb=" N   ARG A 107 " --> pdb=" O   ALA A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 122
      removed outlier: 4.309A  pdb=" N   PHE A 118 " --> pdb=" O   MET A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 130
    Processing helix  chain 'A' and resid 130 through 157
      removed outlier: 4.235A  pdb=" N   ALA A 134 " --> pdb=" O   LEU A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 179
      removed outlier: 3.721A  pdb=" N   VAL A 178 " --> pdb=" O   LEU A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 200
      removed outlier: 3.714A  pdb=" N   VAL A 190 " --> pdb=" O   TYR A 186 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   PHE A 193 " --> pdb=" O   VAL A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 208
    Processing helix  chain 'A' and resid 233 through 235
      No H-bonds generated for 'chain 'A' and resid 233 through 235'
    Processing helix  chain 'A' and resid 236 through 250
    Processing helix  chain 'A' and resid 254 through 262
    Processing helix  chain 'A' and resid 266 through 297
      removed outlier: 4.168A  pdb=" N   ALA A 270 " --> pdb=" O   SER A 266 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   PHE A 275 " --> pdb=" O   GLN A 271 " (cutoff:3.500A)
      Proline residue:  A 287  - end of helix
    Processing helix  chain 'A' and resid 309 through 314
    Processing helix  chain 'A' and resid 315 through 318
    Processing helix  chain 'A' and resid 319 through 327
      removed outlier: 3.677A  pdb=" N   GLN A 325 " --> pdb=" O   PRO A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 363
      removed outlier: 3.871A  pdb=" N   PHE A 335 " --> pdb=" O   TYR A 331 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ARG A 361 " --> pdb=" O   SER A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 399
      removed outlier: 3.561A  pdb=" N   PHE A 386 " --> pdb=" O   ARG A 382 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   THR A 399 " --> pdb=" O   MET A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 426
      Proline residue:  A 419  - end of helix
    Processing helix  chain 'A' and resid 431 through 448
      removed outlier: 3.852A  pdb=" N   ALA A 437 " --> pdb=" O   TYR A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 505
      removed outlier: 4.106A  pdb=" N   MET A 484 " --> pdb=" O   LYS A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 512
      removed outlier: 3.725A  pdb=" N   LEU A 511 " --> pdb=" O   PRO A 508 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 29
      removed outlier: 3.548A  pdb=" N   LEU B   8 " --> pdb=" O   HIS B   4 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 37 through 45
    Processing helix  chain 'B' and resid 46 through 48
      No H-bonds generated for 'chain 'B' and resid 46 through 48'
    Processing helix  chain 'B' and resid 50 through 63
      removed outlier: 3.529A  pdb=" N   VAL B  63 " --> pdb=" O   THR B  59 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 77
      removed outlier: 3.815A  pdb=" N   THR B  71 " --> pdb=" O   TYR B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 102
    Processing helix  chain 'B' and resid 103 through 109
      removed outlier: 3.645A  pdb=" N   ARG B 107 " --> pdb=" O   ALA B 103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 122
      removed outlier: 4.309A  pdb=" N   PHE B 118 " --> pdb=" O   MET B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 130
    Processing helix  chain 'B' and resid 130 through 157
      removed outlier: 4.235A  pdb=" N   ALA B 134 " --> pdb=" O   LEU B 130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 179
      removed outlier: 3.721A  pdb=" N   VAL B 178 " --> pdb=" O   LEU B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 200
      removed outlier: 3.714A  pdb=" N   VAL B 190 " --> pdb=" O   TYR B 186 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   PHE B 193 " --> pdb=" O   VAL B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 208
    Processing helix  chain 'B' and resid 233 through 235
      No H-bonds generated for 'chain 'B' and resid 233 through 235'
    Processing helix  chain 'B' and resid 236 through 250
    Processing helix  chain 'B' and resid 254 through 262
    Processing helix  chain 'B' and resid 266 through 297
      removed outlier: 4.168A  pdb=" N   ALA B 270 " --> pdb=" O   SER B 266 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   PHE B 275 " --> pdb=" O   GLN B 271 " (cutoff:3.500A)
      Proline residue:  B 287  - end of helix
    Processing helix  chain 'B' and resid 309 through 314
    Processing helix  chain 'B' and resid 315 through 318
    Processing helix  chain 'B' and resid 319 through 327
      removed outlier: 3.677A  pdb=" N   GLN B 325 " --> pdb=" O   PRO B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 363
      removed outlier: 3.871A  pdb=" N   PHE B 335 " --> pdb=" O   TYR B 331 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ARG B 361 " --> pdb=" O   SER B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 399
      removed outlier: 3.561A  pdb=" N   PHE B 386 " --> pdb=" O   ARG B 382 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   THR B 399 " --> pdb=" O   MET B 395 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 401 through 426
      Proline residue:  B 419  - end of helix
    Processing helix  chain 'B' and resid 431 through 448
      removed outlier: 3.852A  pdb=" N   ALA B 437 " --> pdb=" O   TYR B 433 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 478 through 505
      removed outlier: 4.106A  pdb=" N   MET B 484 " --> pdb=" O   LYS B 480 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 508 through 512
      removed outlier: 3.725A  pdb=" N   LEU B 511 " --> pdb=" O   PRO B 508 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 466 through 467
    Processing sheet with id=AA2, first strand: chain 'B' and resid 466 through 467

    552 hydrogen bonds defined for protein.
    1638 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: 0.81

  Time building geometry restraints manager: 0.86 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1255
        1.32 -     1.45: 2473
        1.45 -     1.57: 4730
        1.57 -     1.69: 0
        1.69 -     1.81: 70
  Bond restraints: 8528
  Sorted by residual:
  bond pdb=" CB  ASP B 411 "
       pdb=" CG  ASP B 411 "
    ideal  model  delta    sigma   weight residual
    1.516  1.447  0.069 2.50e-02 1.60e+03 7.58e+00
  bond pdb=" CB  ASP A 411 "
       pdb=" CG  ASP A 411 "
    ideal  model  delta    sigma   weight residual
    1.516  1.447  0.069 2.50e-02 1.60e+03 7.58e+00
  bond pdb=" CA  ASP B 411 "
       pdb=" C   ASP B 411 "
    ideal  model  delta    sigma   weight residual
    1.524  1.497  0.027 1.27e-02 6.20e+03 4.39e+00
  bond pdb=" CA  ASP A 411 "
       pdb=" C   ASP A 411 "
    ideal  model  delta    sigma   weight residual
    1.524  1.497  0.027 1.27e-02 6.20e+03 4.39e+00
  bond pdb=" N   PHE A 477 "
       pdb=" CA  PHE A 477 "
    ideal  model  delta    sigma   weight residual
    1.457  1.484 -0.028 1.41e-02 5.03e+03 3.83e+00
  ... (remaining 8523 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.68: 11209
        1.68 -     3.36: 345
        3.36 -     5.04: 70
        5.04 -     6.72: 30
        6.72 -     8.41: 6
  Bond angle restraints: 11660
  Sorted by residual:
  angle pdb=" N   LEU A 482 "
        pdb=" CA  LEU A 482 "
        pdb=" C   LEU A 482 "
      ideal   model   delta    sigma   weight residual
     111.28  105.66    5.62 1.09e+00 8.42e-01 2.65e+01
  angle pdb=" N   LEU B 482 "
        pdb=" CA  LEU B 482 "
        pdb=" C   LEU B 482 "
      ideal   model   delta    sigma   weight residual
     111.28  105.67    5.61 1.09e+00 8.42e-01 2.65e+01
  angle pdb=" N   TYR A 364 "
        pdb=" CA  TYR A 364 "
        pdb=" C   TYR A 364 "
      ideal   model   delta    sigma   weight residual
     112.04  118.40   -6.36 1.44e+00 4.82e-01 1.95e+01
  angle pdb=" N   TYR B 364 "
        pdb=" CA  TYR B 364 "
        pdb=" C   TYR B 364 "
      ideal   model   delta    sigma   weight residual
     112.04  118.40   -6.36 1.44e+00 4.82e-01 1.95e+01
  angle pdb=" N   ILE B 332 "
        pdb=" CA  ILE B 332 "
        pdb=" C   ILE B 332 "
      ideal   model   delta    sigma   weight residual
     111.81  108.01    3.80 8.60e-01 1.35e+00 1.95e+01
  ... (remaining 11655 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.42: 4774
       26.42 -    52.84: 300
       52.84 -    79.26: 60
       79.26 -   105.68: 72
      105.68 -   132.10: 32
  Dihedral angle restraints: 5238
    sinusoidal: 2276
      harmonic: 2962
  Sorted by residual:
  dihedral pdb=" CCF AV0 B 601 "
           pdb=" CCQ AV0 B 601 "
           pdb=" OCB AV0 B 601 "
           pdb=" CCS AV0 B 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -112.55   19.55 -132.10     1      3.00e+01 1.11e-03 1.78e+01
  dihedral pdb=" CCF AV0 A 702 "
           pdb=" CCQ AV0 A 702 "
           pdb=" OCB AV0 A 702 "
           pdb=" CCS AV0 A 702 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -112.55   19.55 -132.10     1      3.00e+01 1.11e-03 1.78e+01
  dihedral pdb=" CCH AV0 B 601 "
           pdb=" CCQ AV0 B 601 "
           pdb=" OCB AV0 B 601 "
           pdb=" CCS AV0 B 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     127.39 -100.76 -131.85     1      3.00e+01 1.11e-03 1.78e+01
  ... (remaining 5235 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 1105
       0.055 -    0.110: 227
       0.110 -    0.164: 28
       0.164 -    0.219: 14
       0.219 -    0.274: 2
  Chirality restraints: 1376
  Sorted by residual:
  chirality pdb=" C5  BMA F   3 "
            pdb=" C4  BMA F   3 "
            pdb=" C6  BMA F   3 "
            pdb=" O5  BMA F   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.27 2.00e-01 2.50e+01 1.88e+00
  chirality pdb=" C5  BMA E   3 "
            pdb=" C4  BMA E   3 "
            pdb=" C6  BMA E   3 "
            pdb=" O5  BMA E   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.27 2.00e-01 2.50e+01 1.85e+00
  chirality pdb=" CB  ILE A 252 "
            pdb=" CA  ILE A 252 "
            pdb=" CG1 ILE A 252 "
            pdb=" CG2 ILE A 252 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.21 2.00e-01 2.50e+01 1.07e+00
  ... (remaining 1373 not shown)

  Planarity restraints: 1372
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 455 "   -0.007 2.00e-02 2.50e+03   1.30e-02 3.40e+00
        pdb=" CG  TYR B 455 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 455 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 455 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 455 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 455 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 455 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B 455 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 455 "   -0.007 2.00e-02 2.50e+03   1.30e-02 3.40e+00
        pdb=" CG  TYR A 455 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 455 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 455 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 455 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 455 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 455 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 455 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 455 "   -0.008 2.00e-02 2.50e+03   1.58e-02 2.50e+00
        pdb=" C   TYR A 455 "    0.027 2.00e-02 2.50e+03
        pdb=" O   TYR A 455 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   LEU A 456 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1369 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 887
        2.74 -     3.28: 8846
        3.28 -     3.82: 14360
        3.82 -     4.36: 15495
        4.36 -     4.90: 27129
  Nonbonded interactions: 66717
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  34 "
            pdb=" OE1 GLU B  37 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" OG  SER A  34 "
            pdb=" OE1 GLU A  37 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" OG  SER A  34 "
            pdb=" OE1 GLU A  36 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" OG  SER B  34 "
            pdb=" OE1 GLU B  36 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" O   PHE A 444 "
            pdb=" OG1 THR A 448 "
     model   vdw
     2.281 3.040
  ... (remaining 66712 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: 0.02
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 3 through 517 or resid 704))
  selection = (chain 'B' and (resid 3 through 517 or resid 604))
}
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 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:             1.540
  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:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.360
  Find NCS groups from input model:        0.180
  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:             0.010
  Load rotamer database and sin/cos tables:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
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      :  0.004   0.069   8534  Z= 0.205
  Angle     :  0.744   8.405  11678  Z= 0.365
  Chirality :  0.047   0.274   1376
  Planarity :  0.004   0.037   1370
  Dihedral  : 24.907 132.103   3366
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 15.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 25.30 %
    Favored  : 74.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.74 (0.29), residues: 1026
  helix:  1.49 (0.21), residues: 734
  sheet:  None (None), residues: 0
  loop : -2.18 (0.39), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  38 
 TYR   0.030   0.002   TYR A 455 
 PHE   0.012   0.001   PHE A 118 
 TRP   0.008   0.001   TRP A 300 
 HIS   0.005   0.001   HIS B 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 8528)
  covalent geometry    : angle       0.73438 (11660)
  hydrogen bonds       : bond        0.10692 (  552)
  hydrogen bonds       : angle       4.42392 ( 1638)
  link_BETA1-4         : bond        0.00589 (    4)
  link_BETA1-4         : angle       2.68435 (   12)
  link_NAG-ASN         : bond        0.00508 (    2)
  link_NAG-ASN         : angle       3.89095 (    6)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A  130 LEU cc_start: 0.8802 (mp) cc_final: 0.8563 (mp)
REVERT: A  455 TYR cc_start: 0.5322 (p90) cc_final: 0.5001 (p90)
REVERT: B  130 LEU cc_start: 0.8787 (mp) cc_final: 0.8544 (mp)
REVERT: B  455 TYR cc_start: 0.5323 (p90) cc_final: 0.5000 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 157
  average time/residue: 0.0668
  time to fit residues: 15.4334
Evaluate side-chains
  144 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    9.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:   10.0000
   chunk 100 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 491 ASN
B 491 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.139964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.125618 restraints weight = 15449.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.128329 restraints weight = 8102.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.129960 restraints weight = 5086.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.131299 restraints weight = 3726.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.131985 restraints weight = 2936.446|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.1047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8534  Z= 0.163
  Angle     :  0.771   9.948  11678  Z= 0.344
  Chirality :  0.046   0.235   1376
  Planarity :  0.004   0.030   1370
  Dihedral  : 19.977 147.048   1716
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 23.86 %
    Favored  : 73.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.92 (0.29), residues: 1026
  helix:  1.52 (0.20), residues: 742
  sheet:  None (None), residues: 0
  loop : -1.87 (0.41), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 446 
 TYR   0.013   0.001   TYR A 414 
 PHE   0.009   0.001   PHE B 461 
 TRP   0.008   0.001   TRP B 406 
 HIS   0.002   0.001   HIS B 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 8528)
  covalent geometry    : angle       0.75975 (11660)
  hydrogen bonds       : bond        0.04056 (  552)
  hydrogen bonds       : angle       4.19228 ( 1638)
  link_BETA1-4         : bond        0.00939 (    4)
  link_BETA1-4         : angle       3.08105 (   12)
  link_NAG-ASN         : bond        0.00802 (    2)
  link_NAG-ASN         : angle       4.15736 (    6)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 142
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8865 (mp)
REVERT: A  318 MET cc_start: 0.7228 (ppp) cc_final: 0.6385 (ppp)
REVERT: A  455 TYR cc_start: 0.5447 (p90) cc_final: 0.5181 (p90)
REVERT: B  130 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8863 (mp)
REVERT: B  318 MET cc_start: 0.7220 (ppp) cc_final: 0.6365 (ppp)
REVERT: B  455 TYR cc_start: 0.5448 (p90) cc_final: 0.5184 (p90)
  outliers start: 22
  outliers final: 12
  residues processed: 160
  average time/residue: 0.0576
  time to fit residues: 13.6333
Evaluate side-chains
  141 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 127
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  368 PHE
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  431 ASN
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  368 PHE
Chi-restraints excluded: chain B residue  383 ILE
Chi-restraints excluded: chain B residue  431 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 77 optimal weight:    8.9990
   chunk 56 optimal weight:    0.8980
   chunk 49 optimal weight:    0.7980
   chunk 40 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9980
   chunk 68 optimal weight:    0.2980
   chunk 94 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 72 optimal weight:    0.4980
   chunk 12 optimal weight:    0.7980
   chunk 99 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 362 ASN
B 362 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.142257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.128114 restraints weight = 15228.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.130772 restraints weight = 7939.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.132431 restraints weight = 5001.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.133709 restraints weight = 3661.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.134606 restraints weight = 2886.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.1269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8534  Z= 0.126
  Angle     :  0.650   9.219  11678  Z= 0.301
  Chirality :  0.042   0.234   1376
  Planarity :  0.004   0.029   1370
  Dihedral  : 15.693 158.041   1716
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 21.69 %
    Favored  : 73.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.29), residues: 1026
  helix:  1.54 (0.20), residues: 742
  sheet:  None (None), residues: 0
  loop : -1.81 (0.41), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  38 
 TYR   0.013   0.001   TYR B 439 
 PHE   0.006   0.001   PHE A 461 
 TRP   0.007   0.001   TRP A 300 
 HIS   0.002   0.001   HIS B 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 8528)
  covalent geometry    : angle       0.63811 (11660)
  hydrogen bonds       : bond        0.03737 (  552)
  hydrogen bonds       : angle       4.10641 ( 1638)
  link_BETA1-4         : bond        0.00929 (    4)
  link_BETA1-4         : angle       2.75265 (   12)
  link_NAG-ASN         : bond        0.00679 (    2)
  link_NAG-ASN         : angle       4.08594 (    6)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 158
  time to evaluate  : 0.229 
Fit side-chains
REVERT: A  229 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8245 (mp)
REVERT: A  318 MET cc_start: 0.7294 (ppp) cc_final: 0.6317 (ppp)
REVERT: A  455 TYR cc_start: 0.5460 (p90) cc_final: 0.5192 (p90)
REVERT: B  229 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8238 (mp)
REVERT: B  318 MET cc_start: 0.7287 (ppp) cc_final: 0.6287 (ppp)
REVERT: B  455 TYR cc_start: 0.5442 (p90) cc_final: 0.5174 (p90)
  outliers start: 40
  outliers final: 19
  residues processed: 190
  average time/residue: 0.0594
  time to fit residues: 16.6132
Evaluate side-chains
  160 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 139
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  368 PHE
Chi-restraints excluded: chain A residue  431 ASN
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  153 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  252 ILE
Chi-restraints excluded: chain B residue  368 PHE
Chi-restraints excluded: chain B residue  431 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 43 optimal weight:    7.9990
   chunk 86 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 70 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   chunk 97 optimal weight:    0.0020
   chunk 57 optimal weight:    5.9990
   chunk 99 optimal weight:    0.8980
   overall best weight:    0.7188

-------------------------------------------------------------------------------
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 365 GLN
** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 365 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.141391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.127162 restraints weight = 15684.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.129973 restraints weight = 8010.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.131842 restraints weight = 4959.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.133054 restraints weight = 3520.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.133946 restraints weight = 2776.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.1454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8534  Z= 0.126
  Angle     :  0.652   9.400  11678  Z= 0.303
  Chirality :  0.041   0.239   1376
  Planarity :  0.003   0.026   1370
  Dihedral  : 14.959 156.587   1716
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 11.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 22.65 %
    Favored  : 73.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.95 (0.29), residues: 1026
  helix:  1.55 (0.20), residues: 746
  sheet:  None (None), residues: 0
  loop : -1.94 (0.41), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  38 
 TYR   0.011   0.001   TYR B 439 
 PHE   0.007   0.001   PHE B 140 
 TRP   0.007   0.001   TRP A 300 
 HIS   0.002   0.001   HIS A 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 8528)
  covalent geometry    : angle       0.63954 (11660)
  hydrogen bonds       : bond        0.03649 (  552)
  hydrogen bonds       : angle       4.15143 ( 1638)
  link_BETA1-4         : bond        0.00902 (    4)
  link_BETA1-4         : angle       2.76387 (   12)
  link_NAG-ASN         : bond        0.00680 (    2)
  link_NAG-ASN         : angle       4.12093 (    6)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 149
  time to evaluate  : 0.219 
Fit side-chains
REVERT: A   62 TRP cc_start: 0.7831 (m100) cc_final: 0.7600 (m100)
REVERT: A  116 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7603 (t0)
REVERT: A  229 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8274 (mp)
REVERT: A  318 MET cc_start: 0.7336 (ppp) cc_final: 0.7040 (ppp)
REVERT: A  455 TYR cc_start: 0.5495 (p90) cc_final: 0.5180 (p90)
REVERT: B   62 TRP cc_start: 0.7832 (m100) cc_final: 0.7603 (m100)
REVERT: B  116 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7559 (t0)
REVERT: B  229 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8264 (mp)
REVERT: B  318 MET cc_start: 0.7340 (ppp) cc_final: 0.7035 (ppp)
REVERT: B  455 TYR cc_start: 0.5500 (p90) cc_final: 0.5187 (p90)
  outliers start: 30
  outliers final: 20
  residues processed: 173
  average time/residue: 0.0584
  time to fit residues: 15.0399
Evaluate side-chains
  156 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 132
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  368 PHE
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  431 ASN
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  252 ILE
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  368 PHE
Chi-restraints excluded: chain B residue  383 ILE
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  431 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   chunk 30 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   chunk 46 optimal weight:    0.0980
   chunk 13 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 51 optimal weight:   10.0000
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 191 GLN
B 191 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.141279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.127211 restraints weight = 15516.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.129951 restraints weight = 7936.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.131766 restraints weight = 4931.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.132932 restraints weight = 3527.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.133848 restraints weight = 2816.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.1565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8534  Z= 0.125
  Angle     :  0.643   9.375  11678  Z= 0.302
  Chirality :  0.042   0.238   1376
  Planarity :  0.003   0.026   1370
  Dihedral  : 14.405 156.220   1716
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 24.70 %
    Favored  : 71.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.94 (0.29), residues: 1026
  helix:  1.53 (0.20), residues: 746
  sheet:  None (None), residues: 0
  loop : -1.93 (0.41), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  38 
 TYR   0.013   0.001   TYR B 439 
 PHE   0.006   0.001   PHE B 131 
 TRP   0.007   0.001   TRP A 300 
 HIS   0.002   0.000   HIS A 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 8528)
  covalent geometry    : angle       0.63100 (11660)
  hydrogen bonds       : bond        0.03653 (  552)
  hydrogen bonds       : angle       4.12140 ( 1638)
  link_BETA1-4         : bond        0.00837 (    4)
  link_BETA1-4         : angle       2.67522 (   12)
  link_NAG-ASN         : bond        0.00672 (    2)
  link_NAG-ASN         : angle       4.09193 (    6)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 145
  time to evaluate  : 0.215 
Fit side-chains
REVERT: A  116 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7583 (t0)
REVERT: A  229 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8248 (mp)
REVERT: A  318 MET cc_start: 0.7101 (ppp) cc_final: 0.6800 (ppp)
REVERT: A  455 TYR cc_start: 0.5516 (p90) cc_final: 0.5210 (p90)
REVERT: B  116 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7577 (t0)
REVERT: B  229 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8243 (mp)
REVERT: B  318 MET cc_start: 0.7112 (ppp) cc_final: 0.6806 (ppp)
REVERT: B  455 TYR cc_start: 0.5522 (p90) cc_final: 0.5218 (p90)
  outliers start: 28
  outliers final: 20
  residues processed: 166
  average time/residue: 0.0578
  time to fit residues: 14.1648
Evaluate side-chains
  162 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 138
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  368 PHE
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  431 ASN
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  247 LEU
Chi-restraints excluded: chain B residue  252 ILE
Chi-restraints excluded: chain B residue  368 PHE
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  431 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 77 optimal weight:    7.9990
   chunk 93 optimal weight:    3.9990
   chunk 83 optimal weight:    0.6980
   chunk 75 optimal weight:    6.9990
   chunk 21 optimal weight:    5.9990
   chunk 100 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9990
   chunk 39 optimal weight:    7.9990
   chunk 95 optimal weight:    5.9990
   chunk 36 optimal weight:    4.9990
   chunk 8 optimal weight:    5.9990
   overall best weight:    2.2786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.134208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.120473 restraints weight = 15620.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.123027 restraints weight = 8235.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.124539 restraints weight = 5253.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.125898 restraints weight = 3897.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.126545 restraints weight = 3078.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.1835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   8534  Z= 0.211
  Angle     :  0.747  10.191  11678  Z= 0.350
  Chirality :  0.044   0.234   1376
  Planarity :  0.004   0.026   1370
  Dihedral  : 13.836 155.063   1716
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 23.49 %
    Favored  : 71.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.28), residues: 1026
  helix:  1.28 (0.20), residues: 748
  sheet:  None (None), residues: 0
  loop : -1.88 (0.43), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  38 
 TYR   0.015   0.002   TYR B  67 
 PHE   0.012   0.001   PHE A 258 
 TRP   0.024   0.002   TRP B  62 
 HIS   0.002   0.001   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00490 ( 8528)
  covalent geometry    : angle       0.73537 (11660)
  hydrogen bonds       : bond        0.04346 (  552)
  hydrogen bonds       : angle       4.45350 ( 1638)
  link_BETA1-4         : bond        0.00819 (    4)
  link_BETA1-4         : angle       3.02540 (   12)
  link_NAG-ASN         : bond        0.00685 (    2)
  link_NAG-ASN         : angle       4.02218 (    6)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 137
  time to evaluate  : 0.176 
Fit side-chains
REVERT: A  318 MET cc_start: 0.7407 (ppp) cc_final: 0.7114 (ppp)
REVERT: A  455 TYR cc_start: 0.5776 (p90) cc_final: 0.5477 (p90)
REVERT: B  318 MET cc_start: 0.7406 (ppp) cc_final: 0.7112 (ppp)
REVERT: B  455 TYR cc_start: 0.5780 (p90) cc_final: 0.5483 (p90)
  outliers start: 39
  outliers final: 20
  residues processed: 168
  average time/residue: 0.0633
  time to fit residues: 15.6684
Evaluate side-chains
  147 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 127
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  368 PHE
Chi-restraints excluded: chain A residue  384 THR
Chi-restraints excluded: chain A residue  431 ASN
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  252 ILE
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  368 PHE
Chi-restraints excluded: chain B residue  384 THR
Chi-restraints excluded: chain B residue  431 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 99 optimal weight:    1.9990
   chunk 36 optimal weight:    5.9990
   chunk 34 optimal weight:    0.8980
   chunk 96 optimal weight:    3.9990
   chunk 3 optimal weight:    9.9990
   overall best weight:    1.1784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.138472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.124423 restraints weight = 15722.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.127148 restraints weight = 8059.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.128814 restraints weight = 5032.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.130130 restraints weight = 3662.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.131010 restraints weight = 2876.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.1822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8534  Z= 0.144
  Angle     :  0.673   9.233  11678  Z= 0.316
  Chirality :  0.043   0.234   1376
  Planarity :  0.004   0.026   1370
  Dihedral  : 13.071 154.782   1716
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 24.82 %
    Favored  : 70.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.82 (0.29), residues: 1026
  helix:  1.39 (0.20), residues: 748
  sheet:  None (None), residues: 0
  loop : -1.81 (0.44), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  38 
 TYR   0.014   0.001   TYR A 439 
 PHE   0.008   0.001   PHE A 131 
 TRP   0.008   0.001   TRP B 406 
 HIS   0.001   0.000   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 8528)
  covalent geometry    : angle       0.66192 (11660)
  hydrogen bonds       : bond        0.03937 (  552)
  hydrogen bonds       : angle       4.26899 ( 1638)
  link_BETA1-4         : bond        0.00788 (    4)
  link_BETA1-4         : angle       2.75284 (   12)
  link_NAG-ASN         : bond        0.00629 (    2)
  link_NAG-ASN         : angle       4.00435 (    6)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 136
  time to evaluate  : 0.184 
Fit side-chains
REVERT: A  126 MET cc_start: 0.7412 (mmm) cc_final: 0.7196 (tpt)
REVERT: A  229 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8310 (mp)
REVERT: A  318 MET cc_start: 0.7385 (ppp) cc_final: 0.7071 (ppp)
REVERT: A  368 PHE cc_start: 0.6273 (OUTLIER) cc_final: 0.5878 (t80)
REVERT: A  455 TYR cc_start: 0.5861 (p90) cc_final: 0.5355 (p90)
REVERT: B  126 MET cc_start: 0.7425 (mmm) cc_final: 0.7195 (tpt)
REVERT: B  229 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8306 (mp)
REVERT: B  318 MET cc_start: 0.7392 (ppp) cc_final: 0.7097 (ppp)
REVERT: B  455 TYR cc_start: 0.5879 (p90) cc_final: 0.5381 (p90)
  outliers start: 37
  outliers final: 24
  residues processed: 163
  average time/residue: 0.0612
  time to fit residues: 14.8154
Evaluate side-chains
  165 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 138
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  368 PHE
Chi-restraints excluded: chain A residue  431 ASN
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  153 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  247 LEU
Chi-restraints excluded: chain B residue  252 ILE
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  368 PHE
Chi-restraints excluded: chain B residue  431 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 92 optimal weight:    0.7980
   chunk 69 optimal weight:    0.9980
   chunk 19 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 42 optimal weight:    7.9990
   chunk 94 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9980
   chunk 11 optimal weight:    0.7980
   chunk 55 optimal weight:    0.0670
   chunk 91 optimal weight:    3.9990
   chunk 57 optimal weight:    5.9990
   overall best weight:    0.7318

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.140207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.126119 restraints weight = 15583.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.128899 restraints weight = 7950.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.130523 restraints weight = 4941.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.131922 restraints weight = 3599.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.132505 restraints weight = 2804.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.1835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8534  Z= 0.129
  Angle     :  0.663   9.299  11678  Z= 0.309
  Chirality :  0.042   0.233   1376
  Planarity :  0.003   0.026   1370
  Dihedral  : 11.835 156.419   1716
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 26.39 %
    Favored  : 70.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.88 (0.29), residues: 1026
  helix:  1.46 (0.20), residues: 748
  sheet:  None (None), residues: 0
  loop : -1.87 (0.43), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  38 
 TYR   0.015   0.001   TYR A 439 
 PHE   0.006   0.001   PHE A 131 
 TRP   0.007   0.001   TRP B 300 
 HIS   0.001   0.000   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 8528)
  covalent geometry    : angle       0.65219 (11660)
  hydrogen bonds       : bond        0.03711 (  552)
  hydrogen bonds       : angle       4.20505 ( 1638)
  link_BETA1-4         : bond        0.00750 (    4)
  link_BETA1-4         : angle       2.53993 (   12)
  link_NAG-ASN         : bond        0.00646 (    2)
  link_NAG-ASN         : angle       3.92939 (    6)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 151
  time to evaluate  : 0.175 
Fit side-chains
REVERT: A  182 TYR cc_start: 0.7905 (OUTLIER) cc_final: 0.7605 (m-10)
REVERT: A  229 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8284 (mp)
REVERT: A  318 MET cc_start: 0.7458 (ppp) cc_final: 0.7123 (ppp)
REVERT: A  455 TYR cc_start: 0.5968 (p90) cc_final: 0.5461 (p90)
REVERT: B  182 TYR cc_start: 0.7857 (OUTLIER) cc_final: 0.7557 (m-10)
REVERT: B  229 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8281 (mp)
REVERT: B  318 MET cc_start: 0.7310 (ppp) cc_final: 0.7035 (ppp)
REVERT: B  455 TYR cc_start: 0.5971 (p90) cc_final: 0.5462 (p90)
  outliers start: 28
  outliers final: 22
  residues processed: 167
  average time/residue: 0.0599
  time to fit residues: 14.6968
Evaluate side-chains
  165 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 139
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  182 TYR
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  368 PHE
Chi-restraints excluded: chain A residue  431 ASN
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  182 TYR
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  247 LEU
Chi-restraints excluded: chain B residue  252 ILE
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  368 PHE
Chi-restraints excluded: chain B residue  431 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 56 optimal weight:    0.8980
   chunk 64 optimal weight:    0.7980
   chunk 14 optimal weight:    0.6980
   chunk 73 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 84 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9980
   chunk 80 optimal weight:    2.9990
   chunk 60 optimal weight:    5.9990
   chunk 53 optimal weight:    8.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 162 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.139928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.125918 restraints weight = 15606.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.128607 restraints weight = 7880.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.130520 restraints weight = 4875.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.131597 restraints weight = 3458.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.132547 restraints weight = 2757.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.1835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8534  Z= 0.134
  Angle     :  0.660   9.319  11678  Z= 0.311
  Chirality :  0.042   0.234   1376
  Planarity :  0.004   0.032   1370
  Dihedral  : 11.606 157.387   1716
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 12.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 26.99 %
    Favored  : 69.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.85 (0.29), residues: 1026
  helix:  1.42 (0.20), residues: 748
  sheet:  None (None), residues: 0
  loop : -1.81 (0.43), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  38 
 TYR   0.015   0.001   TYR A 439 
 PHE   0.005   0.001   PHE A 359 
 TRP   0.007   0.001   TRP B 300 
 HIS   0.001   0.000   HIS A 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 8528)
  covalent geometry    : angle       0.64992 (11660)
  hydrogen bonds       : bond        0.03712 (  552)
  hydrogen bonds       : angle       4.20757 ( 1638)
  link_BETA1-4         : bond        0.00756 (    4)
  link_BETA1-4         : angle       2.54876 (   12)
  link_NAG-ASN         : bond        0.00630 (    2)
  link_NAG-ASN         : angle       3.89281 (    6)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 142
  time to evaluate  : 0.180 
Fit side-chains
REVERT: A  229 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8317 (mp)
REVERT: A  318 MET cc_start: 0.7537 (ppp) cc_final: 0.7249 (ppp)
REVERT: A  455 TYR cc_start: 0.5941 (p90) cc_final: 0.5449 (p90)
REVERT: B  229 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8312 (mp)
REVERT: B  318 MET cc_start: 0.7291 (ppp) cc_final: 0.7032 (ppp)
REVERT: B  455 TYR cc_start: 0.5938 (p90) cc_final: 0.5446 (p90)
  outliers start: 29
  outliers final: 23
  residues processed: 162
  average time/residue: 0.0608
  time to fit residues: 14.5038
Evaluate side-chains
  165 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 140
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  368 PHE
Chi-restraints excluded: chain A residue  431 ASN
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  247 LEU
Chi-restraints excluded: chain B residue  252 ILE
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  368 PHE
Chi-restraints excluded: chain B residue  431 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 82 optimal weight:    0.0570
   chunk 85 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9980
   chunk 89 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 98 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0270
   chunk 69 optimal weight:    0.6980
   chunk 79 optimal weight:    0.0010
   overall best weight:    0.3162

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

Flipped N/Q/H residues before XYZ refinement:
B 162 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.141567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.127647 restraints weight = 15369.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.130479 restraints weight = 7888.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.132133 restraints weight = 4874.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.133417 restraints weight = 3528.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.134366 restraints weight = 2762.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.1957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8534  Z= 0.124
  Angle     :  0.679  12.260  11678  Z= 0.316
  Chirality :  0.042   0.237   1376
  Planarity :  0.004   0.033   1370
  Dihedral  : 11.403 158.072   1716
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 27.71 %
    Favored  : 69.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.80 (0.29), residues: 1026
  helix:  1.38 (0.20), residues: 748
  sheet:  None (None), residues: 0
  loop : -1.85 (0.42), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  38 
 TYR   0.014   0.001   TYR A 439 
 PHE   0.004   0.001   PHE B 444 
 TRP   0.008   0.001   TRP B 254 
 HIS   0.001   0.000   HIS B 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 8528)
  covalent geometry    : angle       0.66965 (11660)
  hydrogen bonds       : bond        0.03564 (  552)
  hydrogen bonds       : angle       4.14656 ( 1638)
  link_BETA1-4         : bond        0.00737 (    4)
  link_BETA1-4         : angle       2.39143 (   12)
  link_NAG-ASN         : bond        0.00630 (    2)
  link_NAG-ASN         : angle       3.87417 (    6)

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

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

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2052 Ramachandran restraints generated.
    1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 143
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A  318 MET cc_start: 0.7519 (ppp) cc_final: 0.7102 (ppp)
REVERT: A  455 TYR cc_start: 0.5997 (p90) cc_final: 0.5497 (p90)
REVERT: B  318 MET cc_start: 0.7329 (ppp) cc_final: 0.7086 (ppp)
REVERT: B  455 TYR cc_start: 0.5993 (p90) cc_final: 0.5495 (p90)
  outliers start: 21
  outliers final: 18
  residues processed: 158
  average time/residue: 0.0562
  time to fit residues: 13.2488
Evaluate side-chains
  153 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 135
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  368 PHE
Chi-restraints excluded: chain A residue  431 ASN
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  184 VAL
Chi-restraints excluded: chain B residue  252 ILE
Chi-restraints excluded: chain B residue  330 VAL
Chi-restraints excluded: chain B residue  368 PHE
Chi-restraints excluded: chain B residue  431 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 15 optimal weight:    0.3980
   chunk 56 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9990
   chunk 68 optimal weight:    0.6980
   chunk 66 optimal weight:    7.9990
   chunk 8 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 86 optimal weight:    0.7980
   chunk 60 optimal weight:    5.9990
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.140034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.126244 restraints weight = 15495.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.128860 restraints weight = 7937.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.130725 restraints weight = 4999.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.131846 restraints weight = 3575.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.132774 restraints weight = 2856.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.1916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8534  Z= 0.133
  Angle     :  0.674   9.391  11678  Z= 0.317
  Chirality :  0.042   0.237   1376
  Planarity :  0.004   0.036   1370
  Dihedral  : 11.296 159.022   1716
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 13.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 27.47 %
    Favored  : 70.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.80 (0.29), residues: 1026
  helix:  1.37 (0.20), residues: 748
  sheet:  None (None), residues: 0
  loop : -1.80 (0.43), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  38 
 TYR   0.023   0.001   TYR A 305 
 PHE   0.009   0.001   PHE B 258 
 TRP   0.011   0.001   TRP B 254 
 HIS   0.001   0.000   HIS B 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 8528)
  covalent geometry    : angle       0.66430 (11660)
  hydrogen bonds       : bond        0.03649 (  552)
  hydrogen bonds       : angle       4.17864 ( 1638)
  link_BETA1-4         : bond        0.00745 (    4)
  link_BETA1-4         : angle       2.42767 (   12)
  link_NAG-ASN         : bond        0.00669 (    2)
  link_NAG-ASN         : angle       3.83837 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1043.90 seconds
wall clock time: 18 minutes 56.47 seconds (1136.47 seconds total)