Starting phenix.real_space_refine
on Tue Feb  3 17:51:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9uob_64376/02_2026/9uob_64376.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9uob_64376/02_2026/9uob_64376.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.33
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9uob_64376/02_2026/9uob_64376.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9uob_64376/02_2026/9uob_64376.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9uob_64376/02_2026/9uob_64376.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9uob_64376/02_2026/9uob_64376.map"
  }
  resolution = 3.33
  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=  -0.000 sd=   0.034
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      23      5.16       5
     C    3628      2.51       5
     N     999      2.21       5
     O    1101      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5751
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4237
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 569, 4237
          Classifications: {'peptide': 569}
          Link IDs: {'PTRANS': 35, 'TRANS': 533}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1338
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 175, 1338
          Classifications: {'peptide': 175}
          Link IDs: {'PTRANS': 8, 'TRANS': 166}
    Chain: "C"
      Number of atoms: 176
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 176
          Classifications: {'peptide': 27}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 22}
  Time building chain proxies: 1.45, per 1000 atoms: 0.25
  Number of scatterers: 5751
  At special positions: 0
  Unit cell: (67.15, 85.85, 121.55, 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      23     16.00
     O    1101      8.00
     N     999      7.00
     C    3628      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  58 " - pdb=" SG  CYS A  65 " distance=1.86
    Simple disulfide: pdb=" SG  CYS A 362 " - pdb=" SG  CYS A 388 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 588 " - pdb=" SG  CYS A 603 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  62 " - pdb=" SG  CYS B  69 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  13 " - pdb=" SG  CYS C  25 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.43
  Conformation dependent library (CDL) restraints added in 237.7 milliseconds
  

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1386

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 13 sheets defined
      17.9% alpha, 12.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 30 through 42
      removed outlier: 3.705A  pdb=" N   ILE A  38 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   LYS A  39 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 49
    Processing helix  chain 'A' and resid 87 through 92
      removed outlier: 3.815A  pdb=" N   GLY A  90 " --> pdb=" O   ASP A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 117
      removed outlier: 3.641A  pdb=" N   ALA A 116 " --> pdb=" O   ASP A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 142
      removed outlier: 3.994A  pdb=" N   LEU A 139 " --> pdb=" O   PRO A 136 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   SER A 140 " --> pdb=" O   THR A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 166
      removed outlier: 3.808A  pdb=" N   LEU A 166 " --> pdb=" O   LEU A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 191
    Processing helix  chain 'A' and resid 211 through 215
    Processing helix  chain 'A' and resid 235 through 239
      removed outlier: 3.767A  pdb=" N   LEU A 239 " --> pdb=" O   ILE A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 289
      removed outlier: 3.698A  pdb=" N   PHE A 287 " --> pdb=" O   PRO A 284 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   GLY A 288 " --> pdb=" O   GLU A 285 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   HIS A 289 " --> pdb=" O   ALA A 286 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 284 through 289'
    Processing helix  chain 'A' and resid 406 through 411
      removed outlier: 3.810A  pdb=" N   TRP A 410 " --> pdb=" O   GLU A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 504
      removed outlier: 3.633A  pdb=" N   VAL A 501 " --> pdb=" O   PRO A 498 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   ALA A 502 " --> pdb=" O   SER A 499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 528
      removed outlier: 4.093A  pdb=" N   MET A 528 " --> pdb=" O   LEU A 525 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 546 through 551
    Processing helix  chain 'A' and resid 574 through 578
      removed outlier: 3.681A  pdb=" N   ASP A 578 " --> pdb=" O   ALA A 575 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 32 through 43
    Processing helix  chain 'B' and resid 60 through 64
      removed outlier: 4.228A  pdb=" N   THR B  63 " --> pdb=" O   ASN B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 120
      removed outlier: 3.534A  pdb=" N   LEU B 117 " --> pdb=" O   PRO B 114 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   GLY B 118 " --> pdb=" O   LEU B 115 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LEU B 120 " --> pdb=" O   LEU B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 168
      removed outlier: 3.655A  pdb=" N   LEU B 165 " --> pdb=" O   PRO B 162 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 188 through 193
      removed outlier: 3.514A  pdb=" N   PHE B 191 " --> pdb=" O   THR B 188 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 195 through 199
    Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 65
      removed outlier: 7.019A  pdb=" N   THR A  64 " --> pdb=" O   THR A  72 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   THR A  72 " --> pdb=" O   SER A  97 " (cutoff:3.500A)
      removed outlier: 8.370A  pdb=" N   ASP A  99 " --> pdb=" O   THR A  72 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   LEU A  74 " --> pdb=" O   ASP A  99 " (cutoff:3.500A)
      removed outlier: 7.097A  pdb=" N   LEU A  98 " --> pdb=" O   MET A 125 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 84
      removed outlier: 6.053A  pdb=" N   GLY A  83 " --> pdb=" O   ASP A 106 " (cutoff:3.500A)
      removed outlier: 7.461A  pdb=" N   GLU A 108 " --> pdb=" O   GLY A  83 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   LEU A 105 " --> pdb=" O   TYR A 130 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   ASN A 132 " --> pdb=" O   LEU A 105 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   GLY A 107 " --> pdb=" O   ASN A 132 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 148 through 149
      removed outlier: 7.170A  pdb=" N   LEU A 148 " --> pdb=" O   THR A 173 " (cutoff:3.500A)
      removed outlier: 9.315A  pdb=" N   THR A 244 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
      removed outlier: 9.596A  pdb=" N   LEU A 273 " --> pdb=" O   THR A 244 " (cutoff:3.500A)
      removed outlier: 8.879A  pdb=" N   ALA A 246 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
      removed outlier: 9.489A  pdb=" N   SER A 275 " --> pdb=" O   ALA A 246 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   PHE A 248 " --> pdb=" O   SER A 275 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   LEU A 296 " --> pdb=" O   SER A 321 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   LEU A 320 " --> pdb=" O   ASP A 347 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 156 through 157
      removed outlier: 4.136A  pdb=" N   GLY A 157 " --> pdb=" O   SER A 178 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 229 through 230
      removed outlier: 3.990A  pdb=" N   GLY A 230 " --> pdb=" O   ASN A 251 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 355
      removed outlier: 4.327A  pdb=" N   GLY A 355 " --> pdb=" O   ARG A 376 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 369 through 371
      removed outlier: 7.336A  pdb=" N   LEU A 370 " --> pdb=" O   MET A 395 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 440 through 441
      removed outlier: 6.353A  pdb=" N   LEU A 440 " --> pdb=" O   ILE A 462 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   PHE A 461 " --> pdb=" O   ASN A 487 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 494 through 495
      removed outlier: 5.607A  pdb=" N   GLY A 495 " --> pdb=" O   ALA A 518 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   LEU A 517 " --> pdb=" O   LYS A 540 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'A' and resid 509 through 511
      removed outlier: 7.714A  pdb=" N   LEU A 534 " --> pdb=" O   ASN A 558 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 567
      removed outlier: 3.849A  pdb=" N   ARG A 601 " --> pdb=" O   LEU A 587 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 44 through 46
      removed outlier: 6.780A  pdb=" N   LEU B  85 " --> pdb=" O   ASN B 108 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   SER B 110 " --> pdb=" O   LEU B  85 " (cutoff:3.500A)
      removed outlier: 5.544A  pdb=" N   GLY B  87 " --> pdb=" O   SER B 110 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   ILE B 109 " --> pdb=" O   LYS B 132 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   THR B 134 " --> pdb=" O   ILE B 109 " (cutoff:3.500A)
      removed outlier: 5.545A  pdb=" N   GLY B 111 " --> pdb=" O   THR B 134 " (cutoff:3.500A)
      removed outlier: 7.034A  pdb=" N   GLY B 136 " --> pdb=" O   GLY B 111 " (cutoff:3.500A)
      removed outlier: 6.308A  pdb=" N   PHE B 133 " --> pdb=" O   SER B 156 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   SER B 158 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
      removed outlier: 5.723A  pdb=" N   GLY B 135 " --> pdb=" O   SER B 158 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 67 through 69
      removed outlier: 3.687A  pdb=" N   TYR B 101 " --> pdb=" O   ILE B  76 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ARG B 151 " --> pdb=" O   LEU B 126 " (cutoff:3.500A)
      removed outlier: 8.143A  pdb=" N   LEU B 150 " --> pdb=" O   ASP B 175 " (cutoff:3.500A)

    73 hydrogen bonds defined for protein.
    114 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: 0.69

  Time building geometry restraints manager: 0.55 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1944
        1.34 -     1.46: 1159
        1.46 -     1.58: 2723
        1.58 -     1.70: 0
        1.70 -     1.82: 35
  Bond restraints: 5861
  Sorted by residual:
  bond pdb=" N   ILE A 311 "
       pdb=" CA  ILE A 311 "
    ideal  model  delta    sigma   weight residual
    1.474  1.457  0.017 1.57e-02 4.06e+03 1.22e+00
  bond pdb=" CG  GLU A 214 "
       pdb=" CD  GLU A 214 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 2.50e-02 1.60e+03 9.37e-01
  bond pdb=" CG  PRO A 548 "
       pdb=" CD  PRO A 548 "
    ideal  model  delta    sigma   weight residual
    1.503  1.476  0.027 3.40e-02 8.65e+02 6.23e-01
  bond pdb=" CB  ASP A 578 "
       pdb=" CG  ASP A 578 "
    ideal  model  delta    sigma   weight residual
    1.516  1.536 -0.020 2.50e-02 1.60e+03 6.16e-01
  bond pdb=" N   PHE A 323 "
       pdb=" CA  PHE A 323 "
    ideal  model  delta    sigma   weight residual
    1.457  1.466 -0.009 1.17e-02 7.31e+03 6.14e-01
  ... (remaining 5856 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.57: 7805
        1.57 -     3.15: 155
        3.15 -     4.72: 20
        4.72 -     6.30: 3
        6.30 -     7.87: 2
  Bond angle restraints: 7985
  Sorted by residual:
  angle pdb=" N   ASN A 144 "
        pdb=" CA  ASN A 144 "
        pdb=" C   ASN A 144 "
      ideal   model   delta    sigma   weight residual
     114.16  109.67    4.49 1.48e+00 4.57e-01 9.20e+00
  angle pdb=" N   ILE B  76 "
        pdb=" CA  ILE B  76 "
        pdb=" C   ILE B  76 "
      ideal   model   delta    sigma   weight residual
     113.10  110.42    2.68 9.70e-01 1.06e+00 7.64e+00
  angle pdb=" N   ILE A 311 "
        pdb=" CA  ILE A 311 "
        pdb=" C   ILE A 311 "
      ideal   model   delta    sigma   weight residual
     106.21  109.08   -2.87 1.07e+00 8.73e-01 7.21e+00
  angle pdb=" N   ARG A 313 "
        pdb=" CA  ARG A 313 "
        pdb=" C   ARG A 313 "
      ideal   model   delta    sigma   weight residual
     114.64  110.79    3.85 1.52e+00 4.33e-01 6.41e+00
  angle pdb=" N   ARG A 313 "
        pdb=" CA  ARG A 313 "
        pdb=" CB  ARG A 313 "
      ideal   model   delta    sigma   weight residual
     111.06  115.01   -3.95 1.59e+00 3.96e-01 6.17e+00
  ... (remaining 7980 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 3078
       18.00 -    35.99: 345
       35.99 -    53.99: 85
       53.99 -    71.99: 13
       71.99 -    89.98: 3
  Dihedral angle restraints: 3524
    sinusoidal: 1357
      harmonic: 2167
  Sorted by residual:
  dihedral pdb=" CB  CYS A 362 "
           pdb=" SG  CYS A 362 "
           pdb=" SG  CYS A 388 "
           pdb=" CB  CYS A 388 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   52.01   40.99     1      1.00e+01 1.00e-02 2.35e+01
  dihedral pdb=" CB  CYS A  58 "
           pdb=" SG  CYS A  58 "
           pdb=" SG  CYS A  65 "
           pdb=" CB  CYS A  65 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  129.84  -36.84     1      1.00e+01 1.00e-02 1.92e+01
  dihedral pdb=" CA  LEU A 273 "
           pdb=" C   LEU A 273 "
           pdb=" N   SER A 274 "
           pdb=" CA  SER A 274 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.18  -20.82     0      5.00e+00 4.00e-02 1.73e+01
  ... (remaining 3521 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 540
       0.029 -    0.058: 271
       0.058 -    0.087: 70
       0.087 -    0.116: 33
       0.116 -    0.145: 16
  Chirality restraints: 930
  Sorted by residual:
  chirality pdb=" CA  ILE A 307 "
            pdb=" N   ILE A 307 "
            pdb=" C   ILE A 307 "
            pdb=" CB  ILE A 307 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.25e-01
  chirality pdb=" CA  ILE A 283 "
            pdb=" N   ILE A 283 "
            pdb=" C   ILE A 283 "
            pdb=" CB  ILE A 283 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.94e-01
  chirality pdb=" CA  VAL A 348 "
            pdb=" N   VAL A 348 "
            pdb=" C   VAL A 348 "
            pdb=" CB  VAL A 348 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.90e-01
  ... (remaining 927 not shown)

  Planarity restraints: 1054
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 195 "    0.031 5.00e-02 4.00e+02   4.76e-02 3.63e+00
        pdb=" N   PRO B 196 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO B 196 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 196 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 546 "    0.028 5.00e-02 4.00e+02   4.20e-02 2.82e+00
        pdb=" N   PRO A 547 "   -0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO A 547 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 547 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 214 "   -0.006 2.00e-02 2.50e+03   1.15e-02 1.31e+00
        pdb=" CD  GLU A 214 "    0.020 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 214 "   -0.007 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 214 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 1051 not shown)

  Histogram of nonbonded interaction distances:
        2.43 -     2.93: 2427
        2.93 -     3.42: 5084
        3.42 -     3.91: 8723
        3.91 -     4.41: 9954
        4.41 -     4.90: 16836
  Nonbonded interactions: 43024
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A  78 "
            pdb=" CA  GLY A 102 "
     model   vdw
     2.433 3.440
  nonbonded pdb=" CE2 PHE A 197 "
            pdb=" CD2 LEU A 223 "
     model   vdw
     2.513 3.760
  nonbonded pdb=" CB  ASN A 127 "
            pdb=" OD1 ASP A 151 "
     model   vdw
     2.521 3.440
  nonbonded pdb=" ND2 ASN A  78 "
            pdb=" CG  PRO C   1 "
     model   vdw
     2.522 3.520
  nonbonded pdb=" O   ASP B 139 "
            pdb=" OD1 ASP B 139 "
     model   vdw
     2.575 3.040
  ... (remaining 43019 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.490
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
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      :  0.003   0.176   5866  Z= 0.158
  Angle     :  0.562   7.873   7995  Z= 0.307
  Chirality :  0.041   0.145    930
  Planarity :  0.004   0.048   1054
  Dihedral  : 15.987  89.984   2123
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.86 %
    Favored  : 92.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 23.15 %
    Favored  : 76.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.09 (0.31), residues: 763
  helix: -3.51 (0.37), residues: 122
  sheet: -4.42 (0.41), residues: 113
  loop : -1.12 (0.29), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  43 
 TYR   0.008   0.001   TYR A 299 
 PHE   0.018   0.001   PHE A 323 
 TRP   0.007   0.001   TRP A 237 
 HIS   0.001   0.000   HIS C  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00207 ( 5861)
  covalent geometry    : angle       0.55755 ( 7985)
  SS BOND              : bond        0.07851 (    5)
  SS BOND              : angle       2.06234 (   10)
  hydrogen bonds       : bond        0.30306 (   73)
  hydrogen bonds       : angle       8.21668 (  114)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.215 
Fit side-chains
REVERT: A   60 TRP cc_start: 0.7966 (m-10) cc_final: 0.7086 (m100)
REVERT: A  214 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8071 (mt-10)
REVERT: A  327 LEU cc_start: 0.8158 (mt) cc_final: 0.7951 (mt)
REVERT: B   97 LYS cc_start: 0.8708 (mmtt) cc_final: 0.8186 (mttm)
REVERT: B  116 GLU cc_start: 0.8522 (mp0) cc_final: 0.8214 (mp0)
REVERT: B  175 ASP cc_start: 0.8038 (t70) cc_final: 0.7469 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.0575
  time to fit residues: 6.2422
Evaluate side-chains
  62 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
A 238 ASN
B  42 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.129488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.100086 restraints weight = 7581.950|
|-----------------------------------------------------------------------------|
r_work (start): 0.3132 rms_B_bonded: 2.43
r_work: 0.3020 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2887 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.0912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5866  Z= 0.158
  Angle     :  0.565   5.506   7995  Z= 0.288
  Chirality :  0.043   0.153    930
  Planarity :  0.004   0.036   1054
  Dihedral  :  4.183  26.428    810
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.53 %
    Favored  : 88.47 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 23.15 %
    Favored  : 74.49 %
  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 are not related in a simple way.
  whole: -3.27 (0.30), residues: 763
  helix: -3.40 (0.40), residues: 115
  sheet: -4.34 (0.40), residues: 121
  loop : -1.34 (0.28), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  43 
 TYR   0.016   0.001   TYR A 299 
 PHE   0.017   0.001   PHE A 323 
 TRP   0.004   0.001   TRP A  51 
 HIS   0.003   0.001   HIS C  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 5861)
  covalent geometry    : angle       0.56426 ( 7985)
  SS BOND              : bond        0.00310 (    5)
  SS BOND              : angle       0.83575 (   10)
  hydrogen bonds       : bond        0.04729 (   73)
  hydrogen bonds       : angle       6.28218 (  114)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.210 
Fit side-chains
REVERT: A   40 ARG cc_start: 0.8231 (mmt90) cc_final: 0.7932 (mmt90)
REVERT: A   99 ASP cc_start: 0.8258 (t0) cc_final: 0.8053 (t0)
REVERT: A  245 MET cc_start: 0.9133 (ttm) cc_final: 0.8918 (ttm)
REVERT: B  175 ASP cc_start: 0.8135 (t70) cc_final: 0.7539 (t70)
  outliers start: 15
  outliers final: 6
  residues processed: 80
  average time/residue: 0.0533
  time to fit residues: 6.0699
Evaluate side-chains
  70 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  207 ASP
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain B residue   42 GLN
Chi-restraints excluded: chain C residue   15 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 13 optimal weight:    6.9990
   chunk 51 optimal weight:    4.9990
   chunk 71 optimal weight:    8.9990
   chunk 7 optimal weight:    8.9990
   chunk 33 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 54 optimal weight:    9.9990
   chunk 67 optimal weight:    5.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 238 ASN
** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  15 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.127419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.097698 restraints weight = 7656.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3099 rms_B_bonded: 2.39
r_work: 0.2987 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2860 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8701
moved from start:          0.1338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   5866  Z= 0.263
  Angle     :  0.657   5.641   7995  Z= 0.336
  Chirality :  0.046   0.158    930
  Planarity :  0.004   0.034   1054
  Dihedral  :  4.625  26.964    810
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.89 %
    Favored  : 86.11 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 23.78 %
    Favored  : 73.70 %
  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 are not related in a simple way.
  whole: -3.44 (0.30), residues: 763
  helix: -3.57 (0.37), residues: 116
  sheet: -4.27 (0.36), residues: 134
  loop : -1.40 (0.28), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  43 
 TYR   0.018   0.002   TYR A 299 
 PHE   0.015   0.002   PHE A 323 
 TRP   0.004   0.001   TRP A 237 
 HIS   0.005   0.001   HIS C  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00644 ( 5861)
  covalent geometry    : angle       0.65655 ( 7985)
  SS BOND              : bond        0.00511 (    5)
  SS BOND              : angle       1.18767 (   10)
  hydrogen bonds       : bond        0.05664 (   73)
  hydrogen bonds       : angle       6.12963 (  114)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 66
  time to evaluate  : 0.160 
Fit side-chains
REVERT: A   40 ARG cc_start: 0.8221 (mmt90) cc_final: 0.7966 (mmt90)
REVERT: B  175 ASP cc_start: 0.8504 (t70) cc_final: 0.7997 (t70)
  outliers start: 16
  outliers final: 13
  residues processed: 80
  average time/residue: 0.0602
  time to fit residues: 6.7486
Evaluate side-chains
  77 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  506 LEU
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  134 THR
Chi-restraints excluded: chain C residue   15 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 44 optimal weight:    5.9990
   chunk 24 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 3 optimal weight:    5.9990
   chunk 55 optimal weight:    5.9990
   chunk 15 optimal weight:    0.0040
   chunk 43 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   overall best weight:    1.3996

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

Flipped N/Q/H residues before XYZ refinement:
A 238 ASN
A 441 HIS
** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  95 GLN
C  15 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.129575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.099972 restraints weight = 7693.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.3132 rms_B_bonded: 2.39
r_work: 0.3019 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2891 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8662
moved from start:          0.1314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5866  Z= 0.149
  Angle     :  0.568   5.525   7995  Z= 0.290
  Chirality :  0.043   0.153    930
  Planarity :  0.003   0.032   1054
  Dihedral  :  4.401  23.507    810
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.27 %
    Favored  : 88.73 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 22.20 %
    Favored  : 73.39 %
  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 are not related in a simple way.
  whole: -3.31 (0.30), residues: 763
  helix: -3.43 (0.39), residues: 116
  sheet: -4.18 (0.37), residues: 130
  loop : -1.35 (0.28), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  43 
 TYR   0.014   0.001   TYR A 299 
 PHE   0.013   0.001   PHE A 323 
 TRP   0.002   0.001   TRP A  60 
 HIS   0.003   0.001   HIS C  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 5861)
  covalent geometry    : angle       0.56749 ( 7985)
  SS BOND              : bond        0.00354 (    5)
  SS BOND              : angle       0.88962 (   10)
  hydrogen bonds       : bond        0.04340 (   73)
  hydrogen bonds       : angle       5.95978 (  114)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 65
  time to evaluate  : 0.129 
Fit side-chains
REVERT: B  175 ASP cc_start: 0.8480 (t70) cc_final: 0.7965 (t70)
  outliers start: 28
  outliers final: 12
  residues processed: 89
  average time/residue: 0.0540
  time to fit residues: 6.7233
Evaluate side-chains
  73 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  207 ASP
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  506 LEU
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  177 SER
Chi-restraints excluded: chain C residue   15 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 52 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 21 optimal weight:    0.6980
   chunk 46 optimal weight:    7.9990
   chunk 23 optimal weight:    0.0980
   chunk 10 optimal weight:    1.9990
   chunk 7 optimal weight:    6.9990
   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 238 ASN
** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.129749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.099919 restraints weight = 7833.477|
|-----------------------------------------------------------------------------|
r_work (start): 0.3100 rms_B_bonded: 2.42
r_work: 0.2987 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2858 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8660
moved from start:          0.1406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5866  Z= 0.143
  Angle     :  0.562   5.992   7995  Z= 0.286
  Chirality :  0.043   0.153    930
  Planarity :  0.004   0.047   1054
  Dihedral  :  4.368  23.984    810
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.32 %
    Favored  : 87.68 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 23.94 %
    Favored  : 72.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.30 (0.30), residues: 763
  helix: -3.46 (0.39), residues: 116
  sheet: -4.15 (0.38), residues: 129
  loop : -1.34 (0.28), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 326 
 TYR   0.014   0.001   TYR A 299 
 PHE   0.012   0.001   PHE A 323 
 TRP   0.002   0.000   TRP A  60 
 HIS   0.002   0.001   HIS C  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 5861)
  covalent geometry    : angle       0.56137 ( 7985)
  SS BOND              : bond        0.00343 (    5)
  SS BOND              : angle       0.87554 (   10)
  hydrogen bonds       : bond        0.04160 (   73)
  hydrogen bonds       : angle       5.86612 (  114)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 63
  time to evaluate  : 0.178 
Fit side-chains
REVERT: B  144 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8276 (mt)
REVERT: B  175 ASP cc_start: 0.8500 (t70) cc_final: 0.7987 (t70)
  outliers start: 23
  outliers final: 14
  residues processed: 83
  average time/residue: 0.0632
  time to fit residues: 7.2662
Evaluate side-chains
  75 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  202 CYS
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  506 LEU
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  177 SER
Chi-restraints excluded: chain C residue   15 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 68 optimal weight:    7.9990
   chunk 38 optimal weight:    0.6980
   chunk 50 optimal weight:    6.9990
   chunk 18 optimal weight:    0.3980
   chunk 12 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 45 optimal weight:    4.9990
   chunk 69 optimal weight:    5.9990
   chunk 44 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9980
   overall best weight:    1.8184

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

Flipped N/Q/H residues before XYZ refinement:
A 238 ASN
** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  15 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.128565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.098823 restraints weight = 7775.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.3139 rms_B_bonded: 2.39
r_work: 0.3029 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2902 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8680
moved from start:          0.1515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5866  Z= 0.181
  Angle     :  0.598   5.859   7995  Z= 0.305
  Chirality :  0.044   0.155    930
  Planarity :  0.004   0.031   1054
  Dihedral  :  4.464  24.025    810
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.76 %
    Favored  : 86.24 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 23.62 %
    Favored  : 72.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.19 (0.30), residues: 763
  helix: -3.38 (0.41), residues: 108
  sheet: -4.28 (0.37), residues: 130
  loop : -1.24 (0.28), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 326 
 TYR   0.014   0.001   TYR A 299 
 PHE   0.014   0.001   PHE A 323 
 TRP   0.003   0.001   TRP A 410 
 HIS   0.003   0.001   HIS C  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 ( 5861)
  covalent geometry    : angle       0.59745 ( 7985)
  SS BOND              : bond        0.00403 (    5)
  SS BOND              : angle       0.99516 (   10)
  hydrogen bonds       : bond        0.04515 (   73)
  hydrogen bonds       : angle       5.83292 (  114)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 63
  time to evaluate  : 0.156 
Fit side-chains
REVERT: A   40 ARG cc_start: 0.8108 (mmt90) cc_final: 0.7888 (mmt90)
REVERT: A  195 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8465 (mttm)
REVERT: A  472 MET cc_start: 0.8580 (mtp) cc_final: 0.8371 (mtm)
REVERT: A  567 GLN cc_start: 0.8779 (mp10) cc_final: 0.8348 (mp10)
REVERT: B  144 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8335 (mt)
REVERT: B  175 ASP cc_start: 0.8507 (t70) cc_final: 0.8002 (t70)
  outliers start: 25
  outliers final: 16
  residues processed: 86
  average time/residue: 0.0639
  time to fit residues: 7.5800
Evaluate side-chains
  80 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 62
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  192 THR
Chi-restraints excluded: chain A residue  195 LYS
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  506 LEU
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  177 SER
Chi-restraints excluded: chain C residue   15 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 67 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 13 optimal weight:    6.9990
   chunk 58 optimal weight:    3.9990
   chunk 14 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 1 optimal weight:    6.9990
   chunk 15 optimal weight:    0.1980
   chunk 50 optimal weight:    5.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 238 ASN
** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.130276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.100457 restraints weight = 7789.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.3134 rms_B_bonded: 2.42
r_work: 0.3025 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2899 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8651
moved from start:          0.1488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5866  Z= 0.129
  Angle     :  0.563   6.977   7995  Z= 0.286
  Chirality :  0.043   0.152    930
  Planarity :  0.004   0.031   1054
  Dihedral  :  4.336  23.214    810
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.27 %
    Favored  : 88.73 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 25.04 %
    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 are not related in a simple way.
  whole: -3.25 (0.30), residues: 763
  helix: -3.38 (0.40), residues: 115
  sheet: -4.32 (0.42), residues: 108
  loop : -1.43 (0.28), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 326 
 TYR   0.012   0.001   TYR A 299 
 PHE   0.013   0.001   PHE A 323 
 TRP   0.002   0.000   TRP A  60 
 HIS   0.002   0.001   HIS C  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 5861)
  covalent geometry    : angle       0.56216 ( 7985)
  SS BOND              : bond        0.00308 (    5)
  SS BOND              : angle       0.85942 (   10)
  hydrogen bonds       : bond        0.03862 (   73)
  hydrogen bonds       : angle       5.72280 (  114)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 66
  time to evaluate  : 0.208 
Fit side-chains
REVERT: A   40 ARG cc_start: 0.8108 (mmt90) cc_final: 0.7882 (mmt90)
REVERT: A  472 MET cc_start: 0.8580 (mtp) cc_final: 0.8367 (mtm)
REVERT: A  567 GLN cc_start: 0.8767 (mp10) cc_final: 0.8329 (mp10)
REVERT: B  144 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8324 (mt)
REVERT: B  175 ASP cc_start: 0.8437 (t70) cc_final: 0.7918 (t70)
  outliers start: 20
  outliers final: 13
  residues processed: 84
  average time/residue: 0.0521
  time to fit residues: 6.1416
Evaluate side-chains
  77 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  202 CYS
Chi-restraints excluded: chain A residue  207 ASP
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  506 LEU
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  177 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 13 optimal weight:    0.0770
   chunk 42 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   chunk 0 optimal weight:    9.9990
   chunk 14 optimal weight:    5.9990
   chunk 15 optimal weight:    0.0370
   chunk 16 optimal weight:    0.7980
   chunk 31 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   overall best weight:    0.9818

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

Flipped N/Q/H residues before XYZ refinement:
A 238 ASN
** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.130910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.101151 restraints weight = 7645.979|
|-----------------------------------------------------------------------------|
r_work (start): 0.3144 rms_B_bonded: 2.39
r_work: 0.3034 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2905 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8635
moved from start:          0.1450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5866  Z= 0.115
  Angle     :  0.550   6.425   7995  Z= 0.279
  Chirality :  0.042   0.151    930
  Planarity :  0.004   0.042   1054
  Dihedral  :  4.204  21.930    810
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.14 %
    Favored  : 88.86 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 25.98 %
    Favored  : 71.18 %
  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 are not related in a simple way.
  whole: -3.18 (0.30), residues: 763
  helix: -3.33 (0.41), residues: 115
  sheet: -4.10 (0.44), residues: 109
  loop : -1.42 (0.28), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 326 
 TYR   0.010   0.001   TYR A 299 
 PHE   0.012   0.001   PHE A 323 
 TRP   0.002   0.000   TRP A  51 
 HIS   0.002   0.001   HIS C  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 5861)
  covalent geometry    : angle       0.54945 ( 7985)
  SS BOND              : bond        0.00293 (    5)
  SS BOND              : angle       0.74050 (   10)
  hydrogen bonds       : bond        0.03555 (   73)
  hydrogen bonds       : angle       5.56602 (  114)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 62
  time to evaluate  : 0.125 
Fit side-chains
REVERT: A   40 ARG cc_start: 0.8127 (mmt90) cc_final: 0.7907 (mmt90)
REVERT: A  214 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8013 (mt-10)
REVERT: A  472 MET cc_start: 0.8564 (mtp) cc_final: 0.8359 (mtm)
REVERT: A  567 GLN cc_start: 0.8770 (mp10) cc_final: 0.8343 (mp10)
REVERT: B  144 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8309 (mt)
REVERT: B  175 ASP cc_start: 0.8411 (t70) cc_final: 0.7891 (t70)
  outliers start: 18
  outliers final: 13
  residues processed: 79
  average time/residue: 0.0498
  time to fit residues: 5.5652
Evaluate side-chains
  76 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  192 THR
Chi-restraints excluded: chain A residue  202 CYS
Chi-restraints excluded: chain A residue  207 ASP
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  506 LEU
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  177 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 49 optimal weight:    0.1980
   chunk 2 optimal weight:    0.0670
   chunk 5 optimal weight:    7.9990
   chunk 28 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 67 optimal weight:    0.8980
   chunk 43 optimal weight:    4.9990
   overall best weight:    0.9720

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

Flipped N/Q/H residues before XYZ refinement:
A 238 ASN
** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.131166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.101513 restraints weight = 7669.139|
|-----------------------------------------------------------------------------|
r_work (start): 0.3123 rms_B_bonded: 2.39
r_work: 0.3010 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2881 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8630
moved from start:          0.1465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5866  Z= 0.114
  Angle     :  0.544   6.205   7995  Z= 0.277
  Chirality :  0.042   0.151    930
  Planarity :  0.004   0.042   1054
  Dihedral  :  4.142  22.352    810
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.75 %
    Favored  : 89.25 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 26.30 %
    Favored  : 71.02 %
  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 are not related in a simple way.
  whole: -3.12 (0.31), residues: 763
  helix: -3.27 (0.41), residues: 115
  sheet: -4.18 (0.39), residues: 126
  loop : -1.22 (0.29), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 326 
 TYR   0.010   0.001   TYR A 299 
 PHE   0.011   0.001   PHE A 323 
 TRP   0.002   0.000   TRP A  51 
 HIS   0.002   0.001   HIS C  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 5861)
  covalent geometry    : angle       0.54326 ( 7985)
  SS BOND              : bond        0.00274 (    5)
  SS BOND              : angle       0.72752 (   10)
  hydrogen bonds       : bond        0.03460 (   73)
  hydrogen bonds       : angle       5.45110 (  114)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 64
  time to evaluate  : 0.150 
Fit side-chains
REVERT: A   40 ARG cc_start: 0.8150 (mmt90) cc_final: 0.7917 (mmt90)
REVERT: A  214 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8054 (mt-10)
REVERT: A  567 GLN cc_start: 0.8761 (mp10) cc_final: 0.8330 (mp10)
REVERT: B  144 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8290 (mt)
REVERT: B  175 ASP cc_start: 0.8409 (t70) cc_final: 0.7891 (t70)
  outliers start: 17
  outliers final: 13
  residues processed: 81
  average time/residue: 0.0588
  time to fit residues: 6.5669
Evaluate side-chains
  76 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  192 THR
Chi-restraints excluded: chain A residue  202 CYS
Chi-restraints excluded: chain A residue  207 ASP
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  506 LEU
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  177 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 45 optimal weight:    0.0170
   chunk 17 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   overall best weight:    0.9822

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

Flipped N/Q/H residues before XYZ refinement:
A 238 ASN
** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.129986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.100822 restraints weight = 7785.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.3157 rms_B_bonded: 2.30
r_work: 0.3048 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2919 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.1458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5866  Z= 0.115
  Angle     :  0.546   6.413   7995  Z= 0.278
  Chirality :  0.042   0.151    930
  Planarity :  0.003   0.041   1054
  Dihedral  :  4.123  21.795    810
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.14 %
    Favored  : 88.86 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 27.09 %
    Favored  : 70.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.11 (0.31), residues: 763
  helix: -3.24 (0.41), residues: 115
  sheet: -4.25 (0.40), residues: 124
  loop : -1.21 (0.29), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 326 
 TYR   0.010   0.001   TYR A 299 
 PHE   0.011   0.001   PHE A 323 
 TRP   0.002   0.000   TRP A  51 
 HIS   0.002   0.001   HIS C  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 5861)
  covalent geometry    : angle       0.54572 ( 7985)
  SS BOND              : bond        0.00273 (    5)
  SS BOND              : angle       0.71069 (   10)
  hydrogen bonds       : bond        0.03427 (   73)
  hydrogen bonds       : angle       5.41482 (  114)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.200 
Fit side-chains
REVERT: A   40 ARG cc_start: 0.8187 (mmt90) cc_final: 0.7944 (mmt90)
REVERT: A  214 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8064 (mt-10)
REVERT: A  567 GLN cc_start: 0.8760 (mp10) cc_final: 0.8328 (mp10)
REVERT: B  175 ASP cc_start: 0.8389 (t70) cc_final: 0.7859 (t70)
  outliers start: 14
  outliers final: 13
  residues processed: 77
  average time/residue: 0.0559
  time to fit residues: 6.0352
Evaluate side-chains
  75 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  192 THR
Chi-restraints excluded: chain A residue  202 CYS
Chi-restraints excluded: chain A residue  207 ASP
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  439 THR
Chi-restraints excluded: chain A residue  506 LEU
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  177 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 55 optimal weight:    6.9990
   chunk 33 optimal weight:    4.9990
   chunk 34 optimal weight:    0.6980
   chunk 19 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 73 optimal weight:    9.9990
   chunk 22 optimal weight:    0.0030
   chunk 12 optimal weight:    4.9990
   chunk 66 optimal weight:    0.6980
   chunk 5 optimal weight:    6.9990
   overall best weight:    1.8794

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

Flipped N/Q/H residues before XYZ refinement:
A 238 ASN
** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.128408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.098740 restraints weight = 7643.639|
|-----------------------------------------------------------------------------|
r_work (start): 0.3113 rms_B_bonded: 2.38
r_work: 0.3003 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2876 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8677
moved from start:          0.1616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   5866  Z= 0.187
  Angle     :  0.604   6.209   7995  Z= 0.308
  Chirality :  0.044   0.154    930
  Planarity :  0.004   0.040   1054
  Dihedral  :  4.390  24.644    810
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.63 %
    Favored  : 86.37 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 26.14 %
    Favored  : 70.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.11 (0.31), residues: 763
  helix: -3.18 (0.44), residues: 107
  sheet: -4.40 (0.37), residues: 134
  loop : -1.14 (0.29), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 326 
 TYR   0.015   0.002   TYR A 299 
 PHE   0.014   0.001   PHE A 323 
 TRP   0.003   0.001   TRP A 237 
 HIS   0.003   0.001   HIS C  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 5861)
  covalent geometry    : angle       0.60338 ( 7985)
  SS BOND              : bond        0.00387 (    5)
  SS BOND              : angle       0.95569 (   10)
  hydrogen bonds       : bond        0.04398 (   73)
  hydrogen bonds       : angle       5.65728 (  114)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1360.08 seconds
wall clock time: 23 minutes 57.43 seconds (1437.43 seconds total)