Starting phenix.real_space_refine
on Tue May 20 04:45:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dvn_47212/05_2025/9dvn_47212_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dvn_47212/05_2025/9dvn_47212.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dvn_47212/05_2025/9dvn_47212.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dvn_47212/05_2025/9dvn_47212.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dvn_47212/05_2025/9dvn_47212_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dvn_47212/05_2025/9dvn_47212_trim.cif"
  }
  resolution = 2.75
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.012
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: 6
    Type Number    sf(0)   Gaussians
     P      40      5.49       5
     S      42      5.16       5
     C    6476      2.51       5
     N    1573      2.21       5
     O    1770      1.98       5
     H    9521      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 19422
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 9499
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 571, 9499
          Classifications: {'peptide': 571}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 551}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 9555
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 574, 9555
          Classifications: {'peptide': 574}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 554}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 183
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 183
          Unusual residues: {'CLR': 1, 'CPL': 1, 'I8P': 2, 'PO4': 3}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
    Chain: "B"
      Number of atoms: 183
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 183
          Unusual residues: {'CLR': 1, 'CPL': 1, 'I8P': 2, 'PO4': 3}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 9.46, per 1000 atoms: 0.49
  Number of scatterers: 19422
  At special positions: 0
  Unit cell: (107.3, 93.525, 122.525, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      42     16.00
     P      40     15.00
     O    1770      8.00
     N    1573      7.00
     C    6476      6.00
     H    9521      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 415 " - pdb=" SG  CYS A 440 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 415 " - pdb=" SG  CYS B 440 " 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: 5.05
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2198

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 0 sheets defined
      84.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 11
      removed outlier: 3.646A  pdb=" N   HIS A   6 " --> pdb=" O   LYS A   2 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 12 through 19
      removed outlier: 5.264A  pdb=" N   LYS A  17 " --> pdb=" O   GLU A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 36
    Processing helix  chain 'A' and resid 47 through 98
    Processing helix  chain 'A' and resid 126 through 168
    Processing helix  chain 'A' and resid 170 through 179
    Processing helix  chain 'A' and resid 180 through 182
      No H-bonds generated for 'chain 'A' and resid 180 through 182'
    Processing helix  chain 'A' and resid 183 through 188
    Processing helix  chain 'A' and resid 189 through 206
    Processing helix  chain 'A' and resid 223 through 227
      removed outlier: 3.543A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 258
    Processing helix  chain 'A' and resid 267 through 296
      removed outlier: 4.466A  pdb=" N   GLY A 274 " --> pdb=" O   ARG A 270 " (cutoff:3.500A)
      removed outlier: 4.640A  pdb=" N   GLY A 275 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 304
    Processing helix  chain 'A' and resid 312 through 337
    Processing helix  chain 'A' and resid 345 through 361
      removed outlier: 3.607A  pdb=" N   LEU A 349 " --> pdb=" O   TYR A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 383
    Processing helix  chain 'A' and resid 384 through 387
    Processing helix  chain 'A' and resid 390 through 419
      removed outlier: 5.887A  pdb=" N   VAL A 405 " --> pdb=" O   ASN A 401 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   ILE A 406 " --> pdb=" O   SER A 402 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   LEU A 407 " --> pdb=" O   LEU A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'A' and resid 445 through 471
      Proline residue:  A 455  - end of helix
    Processing helix  chain 'A' and resid 472 through 502
      removed outlier: 4.034A  pdb=" N   HIS A 476 " --> pdb=" O   ARG A 472 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   THR A 486 " --> pdb=" O   LYS A 482 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   PHE A 487 " --> pdb=" O   TYR A 483 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   GLU A 501 " --> pdb=" O   SER A 497 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ARG A 502 " --> pdb=" O   THR A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 532
    Processing helix  chain 'A' and resid 555 through 582
      removed outlier: 3.902A  pdb=" N   TYR A 559 " --> pdb=" O   GLN A 555 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   PHE A 571 " --> pdb=" O   VAL A 567 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   THR A 582 " --> pdb=" O   SER A 578 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 618
      Proline residue:  A 598  - end of helix
    Processing helix  chain 'B' and resid 2 through 11
    Processing helix  chain 'B' and resid 12 through 19
      removed outlier: 5.284A  pdb=" N   LYS B  17 " --> pdb=" O   GLU B  14 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   TYR B  19 " --> pdb=" O   ARG B  16 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 21 through 35
    Processing helix  chain 'B' and resid 47 through 98
    Processing helix  chain 'B' and resid 123 through 168
    Processing helix  chain 'B' and resid 170 through 179
      removed outlier: 3.543A  pdb=" N   ASP B 174 " --> pdb=" O   SER B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 182
      No H-bonds generated for 'chain 'B' and resid 180 through 182'
    Processing helix  chain 'B' and resid 183 through 188
    Processing helix  chain 'B' and resid 189 through 206
    Processing helix  chain 'B' and resid 210 through 219
      removed outlier: 3.730A  pdb=" N   ARG B 217 " --> pdb=" O   LYS B 213 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 227
      removed outlier: 4.321A  pdb=" N   GLN B 227 " --> pdb=" O   GLY B 224 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 258
    Processing helix  chain 'B' and resid 267 through 296
      removed outlier: 5.225A  pdb=" N   GLY B 274 " --> pdb=" O   ARG B 270 " (cutoff:3.500A)
      removed outlier: 4.874A  pdb=" N   GLY B 275 " --> pdb=" O   ILE B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 303
    Processing helix  chain 'B' and resid 312 through 337
    Processing helix  chain 'B' and resid 345 through 360
      removed outlier: 3.542A  pdb=" N   LEU B 349 " --> pdb=" O   TYR B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 383
    Processing helix  chain 'B' and resid 384 through 387
    Processing helix  chain 'B' and resid 390 through 403
    Processing helix  chain 'B' and resid 403 through 419
      removed outlier: 4.255A  pdb=" N   LEU B 407 " --> pdb=" O   LEU B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 445 through 471
      Proline residue:  B 455  - end of helix
    Processing helix  chain 'B' and resid 472 through 502
      removed outlier: 4.274A  pdb=" N   HIS B 476 " --> pdb=" O   ARG B 472 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   THR B 486 " --> pdb=" O   LYS B 482 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   PHE B 487 " --> pdb=" O   TYR B 483 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   GLU B 501 " --> pdb=" O   SER B 497 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   ARG B 502 " --> pdb=" O   THR B 498 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 532
    Processing helix  chain 'B' and resid 555 through 582
      removed outlier: 4.114A  pdb=" N   TYR B 559 " --> pdb=" O   GLN B 555 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   THR B 582 " --> pdb=" O   SER B 578 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 588 through 618
      Proline residue:  B 598  - end of helix

    734 hydrogen bonds defined for protein.
    2169 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: 6.40

  Time building geometry restraints manager: 5.95 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 9501
        1.03 -     1.23: 30
        1.23 -     1.43: 4375
        1.43 -     1.62: 5709
        1.62 -     1.82: 81
  Bond restraints: 19696
  Sorted by residual:
  bond pdb=" O45 I8P B 805 "
       pdb=" PB5 I8P B 805 "
    ideal  model  delta    sigma   weight residual
    1.695  1.584  0.111 2.00e-02 2.50e+03 3.10e+01
  bond pdb=" O45 I8P B 804 "
       pdb=" PB5 I8P B 804 "
    ideal  model  delta    sigma   weight residual
    1.695  1.584  0.111 2.00e-02 2.50e+03 3.08e+01
  bond pdb=" O45 I8P A 805 "
       pdb=" PB5 I8P A 805 "
    ideal  model  delta    sigma   weight residual
    1.695  1.584  0.111 2.00e-02 2.50e+03 3.07e+01
  bond pdb=" O45 I8P A 804 "
       pdb=" PB5 I8P A 804 "
    ideal  model  delta    sigma   weight residual
    1.695  1.584  0.111 2.00e-02 2.50e+03 3.07e+01
  bond pdb=" O3P CPL B 807 "
       pdb=" P   CPL B 807 "
    ideal  model  delta    sigma   weight residual
    1.633  1.740 -0.107 2.00e-02 2.50e+03 2.86e+01
  ... (remaining 19691 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.04: 35093
        3.04 -     6.09: 157
        6.09 -     9.13: 71
        9.13 -    12.17: 22
       12.17 -    15.22: 18
  Bond angle restraints: 35361
  Sorted by residual:
  angle pdb=" O1P CPL B 807 "
        pdb=" P   CPL B 807 "
        pdb=" O2P CPL B 807 "
      ideal   model   delta    sigma   weight residual
     119.55  134.77  -15.22 3.00e+00 1.11e-01 2.57e+01
  angle pdb=" O1P CPL A 807 "
        pdb=" P   CPL A 807 "
        pdb=" O2P CPL A 807 "
      ideal   model   delta    sigma   weight residual
     119.55  134.75  -15.20 3.00e+00 1.11e-01 2.57e+01
  angle pdb=" O65 I8P A 804 "
        pdb=" PB5 I8P A 804 "
        pdb=" O75 I8P A 804 "
      ideal   model   delta    sigma   weight residual
     113.85   99.79   14.06 3.00e+00 1.11e-01 2.20e+01
  angle pdb=" O65 I8P B 804 "
        pdb=" PB5 I8P B 804 "
        pdb=" O75 I8P B 804 "
      ideal   model   delta    sigma   weight residual
     113.85   99.80   14.05 3.00e+00 1.11e-01 2.19e+01
  angle pdb=" O65 I8P A 805 "
        pdb=" PB5 I8P A 805 "
        pdb=" O75 I8P A 805 "
      ideal   model   delta    sigma   weight residual
     113.85   99.86   13.99 3.00e+00 1.11e-01 2.17e+01
  ... (remaining 35356 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.68: 9163
       34.68 -    69.36: 388
       69.36 -   104.04: 23
      104.04 -   138.72: 10
      138.72 -   173.40: 5
  Dihedral angle restraints: 9589
    sinusoidal: 5178
      harmonic: 4411
  Sorted by residual:
  dihedral pdb=" O35 I8P B 805 "
           pdb=" O45 I8P B 805 "
           pdb=" PA5 I8P B 805 "
           pdb=" PB5 I8P B 805 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -10.77  162.63 -173.40     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C1  I8P A 804 "
           pdb=" O11 I8P A 804 "
           pdb=" PA1 I8P A 804 "
           pdb=" O41 I8P A 804 "
      ideal   model   delta sinusoidal    sigma   weight residual
     309.75  162.66  147.09     1      3.00e+01 1.11e-03 1.96e+01
  dihedral pdb=" C3  CPL A 807 "
           pdb=" C1  CPL A 807 "
           pdb=" C2  CPL A 807 "
           pdb=" O3P CPL A 807 "
      ideal   model   delta sinusoidal    sigma   weight residual
      72.09  -73.55  145.64     1      3.00e+01 1.11e-03 1.95e+01
  ... (remaining 9586 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 1356
       0.072 -    0.144: 112
       0.144 -    0.216: 7
       0.216 -    0.288: 3
       0.288 -    0.360: 8
  Chirality restraints: 1486
  Sorted by residual:
  chirality pdb=" C17 CLR B 806 "
            pdb=" C13 CLR B 806 "
            pdb=" C16 CLR B 806 "
            pdb=" C20 CLR B 806 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.91   -0.36 2.00e-01 2.50e+01 3.24e+00
  chirality pdb=" C17 CLR A 806 "
            pdb=" C13 CLR A 806 "
            pdb=" C16 CLR A 806 "
            pdb=" C20 CLR A 806 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.91   -0.36 2.00e-01 2.50e+01 3.17e+00
  chirality pdb=" C2  CPL A 807 "
            pdb=" C1  CPL A 807 "
            pdb=" C3  CPL A 807 "
            pdb=" O2  CPL A 807 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.65    0.34 2.00e-01 2.50e+01 2.84e+00
  ... (remaining 1483 not shown)

  Planarity restraints: 2750
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 604 "   -0.002 9.50e-02 1.11e+02   1.48e-01 4.93e+02
        pdb=" NE  ARG B 604 "    0.187 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 604 "    0.066 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 604 "   -0.016 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 604 "   -0.014 2.00e-02 2.50e+03
        pdb="HH11 ARG B 604 "   -0.195 2.00e-02 2.50e+03
        pdb="HH12 ARG B 604 "    0.062 2.00e-02 2.50e+03
        pdb="HH21 ARG B 604 "   -0.280 2.00e-02 2.50e+03
        pdb="HH22 ARG B 604 "    0.192 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 604 "   -0.175 9.50e-02 1.11e+02   1.19e-01 2.47e+02
        pdb=" NE  ARG A 604 "   -0.130 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 604 "   -0.040 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 604 "    0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 604 "    0.018 2.00e-02 2.50e+03
        pdb="HH11 ARG A 604 "    0.191 2.00e-02 2.50e+03
        pdb="HH12 ARG A 604 "   -0.117 2.00e-02 2.50e+03
        pdb="HH21 ARG A 604 "    0.152 2.00e-02 2.50e+03
        pdb="HH22 ARG A 604 "   -0.071 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 482 "   -0.013 2.00e-02 2.50e+03   2.43e-02 5.92e+00
        pdb=" N   TYR A 483 "    0.042 2.00e-02 2.50e+03
        pdb=" CA  TYR A 483 "   -0.011 2.00e-02 2.50e+03
        pdb=" H   TYR A 483 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 2747 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 1281
        2.20 -     2.80: 39347
        2.80 -     3.40: 56339
        3.40 -     4.00: 71585
        4.00 -     4.60: 110148
  Nonbonded interactions: 278700
  Sorted by model distance:
  nonbonded pdb=" O   THR A 203 "
            pdb=" H   GLY A 209 "
     model   vdw
     1.605 2.450
  nonbonded pdb=" O   ILE B 271 "
            pdb=" HH  TYR B 352 "
     model   vdw
     1.616 2.450
  nonbonded pdb=" O   ILE A 271 "
            pdb=" HH  TYR A 352 "
     model   vdw
     1.622 2.450
  nonbonded pdb="HH12 ARG A 270 "
            pdb=" O2  PO4 A 803 "
     model   vdw
     1.635 2.450
  nonbonded pdb=" OD1 ASP A 566 "
            pdb="HH11 ARG A 603 "
     model   vdw
     1.637 2.450
  ... (remaining 278695 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 98 or (resid 125 and (name N or name CA or name  \ 
C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 
2 or name HA or name HB2 or name HB3)) or resid 126 through 157 or (resid 158 an \ 
d (name N or name CA or name C or name O or name CB or name CG or name CD or nam \ 
e CE or name NZ or name H or name HA or name HB2 or name HB3 or name HG2 or name \ 
 HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ1 or name HZ2)) o \ 
r resid 159 through 625 or resid 801 through 807))
  selection = (chain 'B' and (resid 1 through 98 or (resid 125 and (name N or name CA or name  \ 
C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 
2 or name HA or name HB2 or name HB3)) or resid 126 through 625 or resid 801 thr \ 
ough 807))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.710
  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:             0.310
  Extract box with map and model:          0.780
  Check model and map are aligned:         0.120
  Set scattering table:                    0.140
  Process input model:                     39.730
  Find NCS groups from input model:        0.620
  Set up NCS constraints:                  0.060
  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:10.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   56.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
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      :  0.006   0.111  10177  Z= 0.302
  Angle     :  1.050  15.215  13842  Z= 0.402
  Chirality :  0.046   0.360   1486
  Planarity :  0.004   0.112   1653
  Dihedral  : 19.741 173.403   3970
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 17.71 %
    Favored  : 81.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.70 (0.26), residues: 1125
  helix:  3.39 (0.17), residues: 867
  sheet:  None (None), residues: 0
  loop : -1.13 (0.40), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 327 
 HIS   0.004   0.001   HIS A 387 
 PHE   0.022   0.001   PHE B   3 
 TYR   0.007   0.001   TYR A 518 
 ARG   0.010   0.000   ARG B 604 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10473 (  734)
  hydrogen bonds       : angle       4.71129 ( 2169)
  SS BOND              : bond        0.00193 (    2)
  SS BOND              : angle       0.61141 (    4)
  covalent geometry    : bond        0.00598 (10175)
  covalent geometry    : angle       1.05026 (13838)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  158 is missing expected H atoms. Skipping.
Evaluate side-chains
  123 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 1.419 
Fit side-chains
   revert: symmetry clash
REVERT: A  582 THR cc_start: 0.6376 (p) cc_final: 0.5982 (p)
REVERT: A  613 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7234 (tt0)
REVERT: B   11 ILE cc_start: 0.7956 (mt) cc_final: 0.7326 (pt)
REVERT: B  129 LYS cc_start: 0.6615 (mttt) cc_final: 0.6150 (tttt)
REVERT: B  213 LYS cc_start: 0.7150 (ttmm) cc_final: 0.6517 (tttt)
REVERT: B  283 PHE cc_start: 0.7913 (t80) cc_final: 0.7550 (m-80)
REVERT: B  394 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.8010 (t80)
REVERT: B  417 TYR cc_start: 0.7188 (t80) cc_final: 0.6019 (m-80)
  outliers start: 10
  outliers final: 2
  residues processed: 122
  average time/residue: 2.2976
  time to fit residues: 304.0097
Evaluate side-chains
  78 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 74
  time to evaluate  : 1.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  609 PHE
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain B residue  394 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.9980
   chunk 86 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   chunk 66 optimal weight:    0.5980
   chunk 103 optimal weight:    1.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 401 ASN
A 476 HIS
B  21 GLN
B 476 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.210020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.151794 restraints weight = 24997.306|
|-----------------------------------------------------------------------------|
r_work (start): 0.3659 rms_B_bonded: 1.72
r_work: 0.3500 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3392 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.1590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10177  Z= 0.152
  Angle     :  0.537   7.376  13842  Z= 0.278
  Chirality :  0.036   0.217   1486
  Planarity :  0.004   0.048   1653
  Dihedral  : 16.765 168.576   1745
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 17.71 %
    Favored  : 80.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.47 (0.25), residues: 1125
  helix:  3.26 (0.16), residues: 856
  sheet:  None (None), residues: 0
  loop : -1.13 (0.39), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 528 
 HIS   0.004   0.001   HIS B 441 
 PHE   0.026   0.002   PHE A 605 
 TYR   0.012   0.002   TYR B 272 
 ARG   0.016   0.001   ARG B 604 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04700 (  734)
  hydrogen bonds       : angle       4.23797 ( 2169)
  SS BOND              : bond        0.00516 (    2)
  SS BOND              : angle       1.41652 (    4)
  covalent geometry    : bond        0.00326 (10175)
  covalent geometry    : angle       0.53670 (13838)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  158 is missing expected H atoms. Skipping.
Evaluate side-chains
  103 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 1.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    2 LYS cc_start: 0.7823 (mtpp) cc_final: 0.7206 (mtmm)
REVERT: A  349 LEU cc_start: 0.8426 (tp) cc_final: 0.8202 (tp)
REVERT: B   11 ILE cc_start: 0.7858 (mt) cc_final: 0.7012 (pt)
REVERT: B  129 LYS cc_start: 0.6240 (mttt) cc_final: 0.5755 (tttt)
REVERT: B  213 LYS cc_start: 0.7079 (ttmm) cc_final: 0.6266 (tttt)
REVERT: B  394 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.8114 (t80)
REVERT: B  417 TYR cc_start: 0.7435 (t80) cc_final: 0.6047 (m-80)
  outliers start: 17
  outliers final: 6
  residues processed: 101
  average time/residue: 2.4435
  time to fit residues: 268.2486
Evaluate side-chains
  86 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 79
  time to evaluate  : 1.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  445 TYR
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  548 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 66 optimal weight:    7.9990
   chunk 104 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 102 optimal weight:    0.0370
   chunk 58 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 80 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.9060

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

Flipped N/Q/H residues before XYZ refinement:
A 401 ASN
B 288 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.202897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.138958 restraints weight = 24968.803|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 1.46
r_work: 0.3442 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3332 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.2293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10177  Z= 0.148
  Angle     :  0.503   7.746  13842  Z= 0.263
  Chirality :  0.034   0.177   1486
  Planarity :  0.004   0.034   1653
  Dihedral  : 15.765 166.027   1740
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 15.63 %
    Favored  : 82.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.28 (0.25), residues: 1125
  helix:  3.06 (0.16), residues: 872
  sheet:  None (None), residues: 0
  loop : -1.28 (0.39), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 514 
 HIS   0.005   0.001   HIS A 476 
 PHE   0.028   0.002   PHE A 605 
 TYR   0.014   0.001   TYR A 352 
 ARG   0.009   0.001   ARG B 604 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04895 (  734)
  hydrogen bonds       : angle       4.10035 ( 2169)
  SS BOND              : bond        0.00569 (    2)
  SS BOND              : angle       1.34632 (    4)
  covalent geometry    : bond        0.00319 (10175)
  covalent geometry    : angle       0.50252 (13838)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  158 is missing expected H atoms. Skipping.
Evaluate side-chains
  106 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 83
  time to evaluate  : 1.570 
Fit side-chains
   revert: symmetry clash
REVERT: A    2 LYS cc_start: 0.7958 (mtpp) cc_final: 0.7494 (mttp)
REVERT: A  137 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.6354 (tm-30)
REVERT: A  405 VAL cc_start: 0.8164 (OUTLIER) cc_final: 0.7887 (t)
REVERT: B  129 LYS cc_start: 0.6289 (mttt) cc_final: 0.5753 (tttt)
REVERT: B  394 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.8251 (t80)
REVERT: B  417 TYR cc_start: 0.7626 (t80) cc_final: 0.6153 (m-80)
REVERT: B  472 ARG cc_start: 0.8209 (mtp-110) cc_final: 0.7961 (mtp85)
  outliers start: 23
  outliers final: 10
  residues processed: 101
  average time/residue: 2.1766
  time to fit residues: 240.9217
Evaluate side-chains
  92 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 79
  time to evaluate  : 1.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  590 ASP
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  401 ASN
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  548 ARG
Chi-restraints excluded: chain B residue  582 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 9 optimal weight:    7.9990
   chunk 108 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 96 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0040
   chunk 25 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 92 optimal weight:    0.8980
   overall best weight:    0.9796

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

Flipped N/Q/H residues before XYZ refinement:
A  21 GLN
A 401 ASN
A 576 GLN
B  21 GLN
B 152 ASN
B 310 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.200426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.136554 restraints weight = 24955.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.3505 rms_B_bonded: 1.42
r_work: 0.3391 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3279 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.2876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10177  Z= 0.154
  Angle     :  0.514   7.868  13842  Z= 0.271
  Chirality :  0.035   0.204   1486
  Planarity :  0.004   0.043   1653
  Dihedral  : 15.337 161.805   1740
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 15.53 %
    Favored  : 82.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.13 (0.25), residues: 1125
  helix:  2.96 (0.16), residues: 872
  sheet:  None (None), residues: 0
  loop : -1.34 (0.39), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 514 
 HIS   0.003   0.001   HIS A 299 
 PHE   0.027   0.002   PHE A 605 
 TYR   0.012   0.002   TYR A 352 
 ARG   0.007   0.001   ARG B 604 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04894 (  734)
  hydrogen bonds       : angle       4.10373 ( 2169)
  SS BOND              : bond        0.00633 (    2)
  SS BOND              : angle       1.71348 (    4)
  covalent geometry    : bond        0.00338 (10175)
  covalent geometry    : angle       0.51312 (13838)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  158 is missing expected H atoms. Skipping.
Evaluate side-chains
  101 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 79
  time to evaluate  : 2.009 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  137 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6473 (tm-30)
REVERT: B  129 LYS cc_start: 0.6250 (mttt) cc_final: 0.5754 (tttt)
REVERT: B  213 LYS cc_start: 0.7428 (tppt) cc_final: 0.6403 (tttt)
REVERT: B  394 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.8291 (t80)
REVERT: B  417 TYR cc_start: 0.7729 (t80) cc_final: 0.6320 (m-80)
REVERT: B  472 ARG cc_start: 0.8305 (mtp-110) cc_final: 0.8057 (mtp85)
  outliers start: 22
  outliers final: 12
  residues processed: 95
  average time/residue: 2.1945
  time to fit residues: 228.2677
Evaluate side-chains
  90 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 1.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  590 ASP
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  401 ASN
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  548 ARG
Chi-restraints excluded: chain B residue  552 VAL
Chi-restraints excluded: chain B residue  577 ILE
Chi-restraints excluded: chain B residue  582 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 62 optimal weight:    6.9990
   chunk 38 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 106 optimal weight:    0.8980
   chunk 26 optimal weight:    0.0670
   chunk 46 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.9322

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

Flipped N/Q/H residues before XYZ refinement:
A 401 ASN
A 576 GLN
B  21 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.203623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.149214 restraints weight = 25222.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.3668 rms_B_bonded: 1.57
r_work: 0.3457 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3355 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.3243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10177  Z= 0.148
  Angle     :  0.497   8.134  13842  Z= 0.262
  Chirality :  0.034   0.185   1486
  Planarity :  0.004   0.054   1653
  Dihedral  : 14.960 155.149   1740
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 15.73 %
    Favored  : 82.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.18 (0.25), residues: 1125
  helix:  3.00 (0.16), residues: 871
  sheet:  None (None), residues: 0
  loop : -1.34 (0.38), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 514 
 HIS   0.004   0.001   HIS A 476 
 PHE   0.026   0.002   PHE A 605 
 TYR   0.011   0.001   TYR A 352 
 ARG   0.004   0.001   ARG A 270 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04842 (  734)
  hydrogen bonds       : angle       4.06289 ( 2169)
  SS BOND              : bond        0.00617 (    2)
  SS BOND              : angle       1.53218 (    4)
  covalent geometry    : bond        0.00322 (10175)
  covalent geometry    : angle       0.49621 (13838)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  158 is missing expected H atoms. Skipping.
Evaluate side-chains
  107 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 84
  time to evaluate  : 1.472 
Fit side-chains
   revert: symmetry clash
REVERT: A    2 LYS cc_start: 0.8051 (mtpp) cc_final: 0.7628 (mttp)
REVERT: A  137 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6579 (tm-30)
REVERT: A  405 VAL cc_start: 0.8150 (OUTLIER) cc_final: 0.7860 (t)
REVERT: A  512 TYR cc_start: 0.7592 (m-10) cc_final: 0.7189 (m-10)
REVERT: B  129 LYS cc_start: 0.6264 (mttt) cc_final: 0.5799 (tttt)
REVERT: B  213 LYS cc_start: 0.7518 (tppt) cc_final: 0.6548 (tttt)
REVERT: B  394 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.8475 (t80)
REVERT: B  417 TYR cc_start: 0.7773 (t80) cc_final: 0.6405 (m-80)
REVERT: B  472 ARG cc_start: 0.8359 (mtp-110) cc_final: 0.8115 (mtp85)
  outliers start: 23
  outliers final: 11
  residues processed: 100
  average time/residue: 2.0581
  time to fit residues: 225.7480
Evaluate side-chains
  90 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 1.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  590 ASP
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  401 ASN
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  548 ARG
Chi-restraints excluded: chain B residue  552 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 95 optimal weight:    2.9990
   chunk 99 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 4 optimal weight:    9.9990
   chunk 97 optimal weight:    0.4980
   chunk 3 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 93 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 89 optimal weight:    0.0670
   overall best weight:    1.3124

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

Flipped N/Q/H residues before XYZ refinement:
A 401 ASN
A 576 GLN
B  18 GLN
B  21 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.202216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.144561 restraints weight = 24849.904|
|-----------------------------------------------------------------------------|
r_work (start): 0.3604 rms_B_bonded: 1.62
r_work: 0.3393 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.3677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10177  Z= 0.183
  Angle     :  0.548   8.347  13842  Z= 0.290
  Chirality :  0.036   0.211   1486
  Planarity :  0.004   0.040   1653
  Dihedral  : 14.912 147.080   1740
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 15.13 %
    Favored  : 82.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.85 (0.25), residues: 1125
  helix:  2.76 (0.16), residues: 870
  sheet:  None (None), residues: 0
  loop : -1.42 (0.38), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 514 
 HIS   0.005   0.001   HIS B 616 
 PHE   0.031   0.002   PHE A 605 
 TYR   0.015   0.002   TYR B 272 
 ARG   0.004   0.001   ARG B 604 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05370 (  734)
  hydrogen bonds       : angle       4.17412 ( 2169)
  SS BOND              : bond        0.00785 (    2)
  SS BOND              : angle       1.76921 (    4)
  covalent geometry    : bond        0.00407 (10175)
  covalent geometry    : angle       0.54734 (13838)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  158 is missing expected H atoms. Skipping.
Evaluate side-chains
  106 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 79
  time to evaluate  : 1.320 
Fit side-chains
   revert: symmetry clash
REVERT: A  137 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6469 (tm-30)
REVERT: A  318 GLU cc_start: 0.8001 (tt0) cc_final: 0.7776 (tt0)
REVERT: A  398 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8270 (m-30)
REVERT: A  405 VAL cc_start: 0.8260 (OUTLIER) cc_final: 0.7903 (t)
REVERT: A  512 TYR cc_start: 0.7584 (m-10) cc_final: 0.7136 (m-80)
REVERT: A  549 GLU cc_start: 0.7935 (pt0) cc_final: 0.7700 (pt0)
REVERT: A  579 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7812 (mp)
REVERT: B   23 GLU cc_start: 0.6410 (mm-30) cc_final: 0.6078 (mp0)
REVERT: B  129 LYS cc_start: 0.6349 (mttt) cc_final: 0.5904 (tttt)
REVERT: B  213 LYS cc_start: 0.7635 (tppt) cc_final: 0.6696 (tttt)
REVERT: B  216 LYS cc_start: 0.8078 (ttpt) cc_final: 0.7621 (ttpp)
REVERT: B  394 PHE cc_start: 0.8953 (OUTLIER) cc_final: 0.8386 (t80)
REVERT: B  417 TYR cc_start: 0.7784 (t80) cc_final: 0.6471 (m-80)
REVERT: B  472 ARG cc_start: 0.8341 (mtp-110) cc_final: 0.8122 (mtp85)
REVERT: B  512 TYR cc_start: 0.7798 (m-10) cc_final: 0.7282 (m-10)
  outliers start: 27
  outliers final: 13
  residues processed: 97
  average time/residue: 2.1325
  time to fit residues: 225.5648
Evaluate side-chains
  95 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 77
  time to evaluate  : 1.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  590 ASP
Chi-restraints excluded: chain B residue  130 ASP
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  401 ASN
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  508 MET
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  548 ARG
Chi-restraints excluded: chain B residue  552 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 100 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   chunk 103 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   chunk 73 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 112 optimal weight:    0.9980
   chunk 96 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   chunk 66 optimal weight:    8.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A  81 GLN
A 401 ASN
A 452 GLN
A 576 GLN
B  21 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.203064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.146462 restraints weight = 24850.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 1.62
r_work: 0.3442 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3339 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.3745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10177  Z= 0.151
  Angle     :  0.505   8.378  13842  Z= 0.267
  Chirality :  0.035   0.197   1486
  Planarity :  0.004   0.038   1653
  Dihedral  : 14.466 142.850   1740
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 15.43 %
    Favored  : 82.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.96 (0.25), residues: 1125
  helix:  2.84 (0.16), residues: 870
  sheet:  None (None), residues: 0
  loop : -1.38 (0.38), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 514 
 HIS   0.004   0.001   HIS A 476 
 PHE   0.026   0.002   PHE A 605 
 TYR   0.011   0.001   TYR A 352 
 ARG   0.003   0.000   ARG B 604 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04929 (  734)
  hydrogen bonds       : angle       4.10948 ( 2169)
  SS BOND              : bond        0.00646 (    2)
  SS BOND              : angle       1.65739 (    4)
  covalent geometry    : bond        0.00329 (10175)
  covalent geometry    : angle       0.50404 (13838)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  158 is missing expected H atoms. Skipping.
Evaluate side-chains
  103 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 80
  time to evaluate  : 1.504 
Fit side-chains
   revert: symmetry clash
REVERT: A  137 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6613 (tm-30)
REVERT: A  405 VAL cc_start: 0.8195 (OUTLIER) cc_final: 0.7879 (t)
REVERT: A  512 TYR cc_start: 0.7660 (m-10) cc_final: 0.7200 (m-80)
REVERT: A  549 GLU cc_start: 0.7997 (pt0) cc_final: 0.7755 (pt0)
REVERT: A  575 ILE cc_start: 0.8320 (mt) cc_final: 0.7909 (tp)
REVERT: A  579 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7805 (mp)
REVERT: B   23 GLU cc_start: 0.6532 (mm-30) cc_final: 0.6142 (mp0)
REVERT: B  129 LYS cc_start: 0.6385 (mttt) cc_final: 0.5953 (tttt)
REVERT: B  213 LYS cc_start: 0.7681 (tppt) cc_final: 0.6743 (tttt)
REVERT: B  216 LYS cc_start: 0.8167 (ttpt) cc_final: 0.7699 (ttpp)
REVERT: B  394 PHE cc_start: 0.8948 (OUTLIER) cc_final: 0.8510 (t80)
REVERT: B  417 TYR cc_start: 0.7807 (t80) cc_final: 0.6496 (m-80)
REVERT: B  508 MET cc_start: 0.7081 (mmp) cc_final: 0.6134 (tpp)
  outliers start: 23
  outliers final: 15
  residues processed: 96
  average time/residue: 2.1076
  time to fit residues: 222.1931
Evaluate side-chains
  96 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 77
  time to evaluate  : 1.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  590 ASP
Chi-restraints excluded: chain B residue   11 ILE
Chi-restraints excluded: chain B residue  185 PHE
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  401 ASN
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  548 ARG
Chi-restraints excluded: chain B residue  552 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 8 optimal weight:    8.9990
   chunk 4 optimal weight:    9.9990
   chunk 71 optimal weight:   10.0000
   chunk 99 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9990
   chunk 110 optimal weight:    3.9990
   chunk 113 optimal weight:    1.9990
   chunk 111 optimal weight:    0.9990
   chunk 94 optimal weight:    1.9990
   overall best weight:    1.3388

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

Flipped N/Q/H residues before XYZ refinement:
A 401 ASN
A 576 GLN
B  21 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.200740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.145962 restraints weight = 24764.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.3620 rms_B_bonded: 1.62
r_work: 0.3411 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3310 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.4061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10177  Z= 0.186
  Angle     :  0.548   8.618  13842  Z= 0.290
  Chirality :  0.036   0.203   1486
  Planarity :  0.004   0.041   1653
  Dihedral  : 14.525 136.678   1740
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 14.94 %
    Favored  : 82.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.76 (0.25), residues: 1125
  helix:  2.70 (0.16), residues: 870
  sheet:  None (None), residues: 0
  loop : -1.44 (0.38), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 514 
 HIS   0.005   0.001   HIS B 616 
 PHE   0.030   0.002   PHE A 605 
 TYR   0.014   0.002   TYR B 272 
 ARG   0.004   0.001   ARG B 604 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05417 (  734)
  hydrogen bonds       : angle       4.17252 ( 2169)
  SS BOND              : bond        0.00759 (    2)
  SS BOND              : angle       1.69611 (    4)
  covalent geometry    : bond        0.00419 (10175)
  covalent geometry    : angle       0.54710 (13838)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  158 is missing expected H atoms. Skipping.
Evaluate side-chains
  105 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 79
  time to evaluate  : 1.322 
Fit side-chains
   revert: symmetry clash
REVERT: A  137 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6638 (tm-30)
REVERT: A  398 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8275 (m-30)
REVERT: A  405 VAL cc_start: 0.8293 (OUTLIER) cc_final: 0.7930 (t)
REVERT: A  579 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7843 (mp)
REVERT: B   23 GLU cc_start: 0.6723 (mm-30) cc_final: 0.6299 (mp0)
REVERT: B  129 LYS cc_start: 0.6240 (mttt) cc_final: 0.5815 (tttt)
REVERT: B  213 LYS cc_start: 0.7769 (tppt) cc_final: 0.6811 (tttt)
REVERT: B  216 LYS cc_start: 0.8194 (ttpt) cc_final: 0.7694 (ttpp)
REVERT: B  394 PHE cc_start: 0.8969 (OUTLIER) cc_final: 0.8450 (t80)
REVERT: B  417 TYR cc_start: 0.7864 (t80) cc_final: 0.6524 (m-80)
REVERT: B  508 MET cc_start: 0.7168 (mmp) cc_final: 0.6070 (tpp)
  outliers start: 26
  outliers final: 15
  residues processed: 98
  average time/residue: 2.2993
  time to fit residues: 245.1783
Evaluate side-chains
  94 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 74
  time to evaluate  : 1.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  590 ASP
Chi-restraints excluded: chain B residue   11 ILE
Chi-restraints excluded: chain B residue  130 ASP
Chi-restraints excluded: chain B residue  185 PHE
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  401 ASN
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  548 ARG
Chi-restraints excluded: chain B residue  552 VAL
Chi-restraints excluded: chain B residue  582 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 77 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 83 optimal weight:    0.7980
   chunk 63 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   chunk 2 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 401 ASN
A 576 GLN
B  21 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.197788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.136205 restraints weight = 25117.035|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 1.37
r_work: 0.3395 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3292 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.4195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10177  Z= 0.183
  Angle     :  0.538   8.568  13842  Z= 0.284
  Chirality :  0.036   0.195   1486
  Planarity :  0.004   0.041   1653
  Dihedral  : 14.303 133.551   1740
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 15.43 %
    Favored  : 82.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.70 (0.25), residues: 1125
  helix:  2.65 (0.16), residues: 871
  sheet:  None (None), residues: 0
  loop : -1.47 (0.38), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 514 
 HIS   0.004   0.001   HIS A 476 
 PHE   0.027   0.002   PHE A 605 
 TYR   0.012   0.002   TYR B 272 
 ARG   0.004   0.001   ARG B 604 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05264 (  734)
  hydrogen bonds       : angle       4.18052 ( 2169)
  SS BOND              : bond        0.00734 (    2)
  SS BOND              : angle       1.73037 (    4)
  covalent geometry    : bond        0.00411 (10175)
  covalent geometry    : angle       0.53730 (13838)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  158 is missing expected H atoms. Skipping.
Evaluate side-chains
  102 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 79
  time to evaluate  : 1.413 
Fit side-chains
   revert: symmetry clash
REVERT: A  137 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6387 (tm-30)
REVERT: A  270 ARG cc_start: 0.8516 (mmt180) cc_final: 0.8273 (mmt180)
REVERT: A  405 VAL cc_start: 0.8238 (OUTLIER) cc_final: 0.7882 (t)
REVERT: A  549 GLU cc_start: 0.7988 (pt0) cc_final: 0.7723 (pt0)
REVERT: A  579 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7713 (mp)
REVERT: B   23 GLU cc_start: 0.6842 (mm-30) cc_final: 0.6371 (mp0)
REVERT: B  129 LYS cc_start: 0.6134 (mttt) cc_final: 0.5718 (tttt)
REVERT: B  193 GLN cc_start: 0.7793 (mm-40) cc_final: 0.7086 (mt0)
REVERT: B  213 LYS cc_start: 0.7755 (tppt) cc_final: 0.6777 (tttt)
REVERT: B  394 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.8494 (t80)
REVERT: B  417 TYR cc_start: 0.7874 (t80) cc_final: 0.6445 (m-80)
REVERT: B  508 MET cc_start: 0.6990 (mmp) cc_final: 0.6002 (tpp)
  outliers start: 23
  outliers final: 14
  residues processed: 97
  average time/residue: 2.3701
  time to fit residues: 248.5444
Evaluate side-chains
  93 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 75
  time to evaluate  : 1.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  590 ASP
Chi-restraints excluded: chain B residue   11 ILE
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  401 ASN
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  548 ARG
Chi-restraints excluded: chain B residue  552 VAL
Chi-restraints excluded: chain B residue  582 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 107 optimal weight:    0.7980
   chunk 104 optimal weight:    2.9990
   chunk 7 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    1.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 401 ASN
A 576 GLN
B  21 GLN
** B  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.197318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.135741 restraints weight = 24984.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.3525 rms_B_bonded: 1.36
r_work: 0.3415 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3308 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
moved from start:          0.4369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10177  Z= 0.187
  Angle     :  0.549   8.643  13842  Z= 0.291
  Chirality :  0.036   0.192   1486
  Planarity :  0.004   0.041   1653
  Dihedral  : 14.358 132.125   1740
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 15.33 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.63 (0.25), residues: 1125
  helix:  2.59 (0.16), residues: 872
  sheet:  None (None), residues: 0
  loop : -1.46 (0.38), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 514 
 HIS   0.005   0.001   HIS A 476 
 PHE   0.029   0.002   PHE A 605 
 TYR   0.013   0.002   TYR B 272 
 ARG   0.004   0.001   ARG A 273 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05359 (  734)
  hydrogen bonds       : angle       4.19060 ( 2169)
  SS BOND              : bond        0.00701 (    2)
  SS BOND              : angle       1.65616 (    4)
  covalent geometry    : bond        0.00420 (10175)
  covalent geometry    : angle       0.54823 (13838)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  158 is missing expected H atoms. Skipping.
Evaluate side-chains
  99 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 76
  time to evaluate  : 1.386 
Fit side-chains
   revert: symmetry clash
REVERT: A  137 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6471 (tm-30)
REVERT: A  405 VAL cc_start: 0.8253 (OUTLIER) cc_final: 0.7892 (t)
REVERT: A  549 GLU cc_start: 0.7952 (pt0) cc_final: 0.7663 (pt0)
REVERT: A  579 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7769 (mp)
REVERT: B   23 GLU cc_start: 0.6899 (mm-30) cc_final: 0.6466 (mp0)
REVERT: B  129 LYS cc_start: 0.6181 (mttt) cc_final: 0.5787 (tttt)
REVERT: B  193 GLN cc_start: 0.7797 (mm-40) cc_final: 0.7136 (mt0)
REVERT: B  213 LYS cc_start: 0.7768 (tppt) cc_final: 0.6815 (tttt)
REVERT: B  394 PHE cc_start: 0.8951 (OUTLIER) cc_final: 0.8459 (t80)
REVERT: B  417 TYR cc_start: 0.7823 (t80) cc_final: 0.6371 (m-80)
REVERT: B  508 MET cc_start: 0.7036 (mmp) cc_final: 0.6083 (tpp)
  outliers start: 23
  outliers final: 14
  residues processed: 94
  average time/residue: 2.3306
  time to fit residues: 237.5733
Evaluate side-chains
  90 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 72
  time to evaluate  : 1.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  590 ASP
Chi-restraints excluded: chain B residue   11 ILE
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  401 ASN
Chi-restraints excluded: chain B residue  405 VAL
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  548 ARG
Chi-restraints excluded: chain B residue  552 VAL
Chi-restraints excluded: chain B residue  582 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 73 optimal weight:    0.0570
   chunk 23 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9980
   chunk 72 optimal weight:    0.7980
   chunk 17 optimal weight:    9.9990
   chunk 18 optimal weight:    2.9990
   chunk 66 optimal weight:    7.9990
   chunk 67 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 82 optimal weight:    1.9990
   overall best weight:    0.7098

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

Flipped N/Q/H residues before XYZ refinement:
A 401 ASN
A 576 GLN
B  21 GLN
** B  70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.201216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.145450 restraints weight = 25090.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.3611 rms_B_bonded: 1.58
r_work: 0.3423 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3313 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.4330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10177  Z= 0.135
  Angle     :  0.502   8.545  13842  Z= 0.265
  Chirality :  0.034   0.183   1486
  Planarity :  0.004   0.041   1653
  Dihedral  : 13.838 131.715   1740
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 15.73 %
    Favored  : 82.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.91 (0.25), residues: 1125
  helix:  2.79 (0.17), residues: 873
  sheet:  None (None), residues: 0
  loop : -1.40 (0.38), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 514 
 HIS   0.003   0.001   HIS A 476 
 PHE   0.026   0.002   PHE A 605 
 TYR   0.009   0.001   TYR B 352 
 ARG   0.003   0.000   ARG A 270 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04715 (  734)
  hydrogen bonds       : angle       4.08448 ( 2169)
  SS BOND              : bond        0.00663 (    2)
  SS BOND              : angle       1.75676 (    4)
  covalent geometry    : bond        0.00290 (10175)
  covalent geometry    : angle       0.50154 (13838)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 12186.23 seconds
wall clock time: 209 minutes 1.33 seconds (12541.33 seconds total)