Starting phenix.real_space_refine
on Wed Sep 17 16:25:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5fn5_3240/09_2025/5fn5_3240.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5fn5_3240/09_2025/5fn5_3240.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/5fn5_3240/09_2025/5fn5_3240.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5fn5_3240/09_2025/5fn5_3240.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/5fn5_3240/09_2025/5fn5_3240.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5fn5_3240/09_2025/5fn5_3240.map"
  }
  resolution = 4.3
  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=   0.007
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      36      5.16       5
     C    6313      2.51       5
     N    1572      2.21       5
     O    1724      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9645
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5222
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 665, 5222
          Classifications: {'peptide': 665}
          Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 627}
    Chain: "B"
      Number of atoms: 1735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1735
          Classifications: {'peptide': 223}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 215}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 43
          Unresolved non-hydrogen angles: 55
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 30
    Chain: "C"
      Number of atoms: 1868
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 243, 1868
          Classifications: {'peptide': 243}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 233}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "D"
      Number of atoms: 820
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 820
          Classifications: {'peptide': 96}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 91}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
  Time building chain proxies: 2.45, per 1000 atoms: 0.25
  Number of scatterers: 9645
  At special positions: 0
  Unit cell: (93.8, 142.8, 96.6, 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      36     16.00
     O    1724      8.00
     N    1572      7.00
     C    6313      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  50 " - pdb=" SG  CYS A  62 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 140 " - pdb=" SG  CYS A 159 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 195 " - pdb=" SG  CYS A 213 " distance=2.07
    Simple disulfide: pdb=" SG  CYS A 230 " - pdb=" SG  CYS A 248 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 586 " - pdb=" SG  CYS A 620 " distance=2.04

  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: 0.93
  Conformation dependent library (CDL) restraints added in 354.0 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2308

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 7 sheets defined
      59.1% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 34 through 41
      removed outlier: 3.842A  pdb=" N   ARG A  38 " --> pdb=" O   ASN A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 88
    Processing helix  chain 'A' and resid 105 through 113
    Processing helix  chain 'A' and resid 142 through 146
      removed outlier: 3.892A  pdb=" N   GLY A 146 " --> pdb=" O   ASP A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 200
      removed outlier: 4.198A  pdb=" N   THR A 189 " --> pdb=" O   ASP A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 240
    Processing helix  chain 'A' and resid 298 through 314
    Processing helix  chain 'A' and resid 337 through 350
    Processing helix  chain 'A' and resid 381 through 387
    Processing helix  chain 'A' and resid 387 through 407
      removed outlier: 3.666A  pdb=" N   GLY A 407 " --> pdb=" O   LYS A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 431
      removed outlier: 4.025A  pdb=" N   ARG A 429 " --> pdb=" O   SER A 425 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 434
      No H-bonds generated for 'chain 'A' and resid 432 through 434'
    Processing helix  chain 'A' and resid 459 through 464
    Processing helix  chain 'A' and resid 474 through 479
      removed outlier: 4.065A  pdb=" N   ASN A 478 " --> pdb=" O   GLU A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 504
      removed outlier: 3.570A  pdb=" N   GLY A 504 " --> pdb=" O   GLU A 500 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 514 through 527
      removed outlier: 3.733A  pdb=" N   VAL A 518 " --> pdb=" O   ASP A 514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 531 through 537
    Processing helix  chain 'A' and resid 541 through 546
    Processing helix  chain 'A' and resid 561 through 575
      removed outlier: 3.541A  pdb=" N   VAL A 566 " --> pdb=" O   ASN A 562 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 582 through 588
    Processing helix  chain 'A' and resid 633 through 638
    Processing helix  chain 'A' and resid 665 through 698
      removed outlier: 5.173A  pdb=" N   ASP A 695 " --> pdb=" O   ASN A 691 " (cutoff:3.500A)
      removed outlier: 5.911A  pdb=" N   VAL A 696 " --> pdb=" O   ALA A 692 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 102
      Proline residue:  B  88  - end of helix
      removed outlier: 3.509A  pdb=" N   LEU B  91 " --> pdb=" O   VAL B  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 190
      removed outlier: 3.676A  pdb=" N   PHE B 179 " --> pdb=" O   PHE B 175 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ILE B 180 " --> pdb=" O   PHE B 176 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   THR B 188 " --> pdb=" O   GLU B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 195 through 214
    Processing helix  chain 'B' and resid 218 through 240
    Processing helix  chain 'B' and resid 244 through 263
    Processing helix  chain 'B' and resid 382 through 398
    Processing helix  chain 'B' and resid 403 through 429
      removed outlier: 3.699A  pdb=" N   THR B 421 " --> pdb=" O   GLY B 417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 435 through 464
      removed outlier: 3.675A  pdb=" N   VAL B 444 " --> pdb=" O   THR B 440 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   PHE B 445 " --> pdb=" O   PHE B 441 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   GLN B 454 " --> pdb=" O   ASP B 450 " (cutoff:3.500A)
      Proline residue:  B 455  - end of helix
    Processing helix  chain 'C' and resid 2 through 24
      Proline residue:  C  16  - end of helix
    Processing helix  chain 'C' and resid 28 through 60
      removed outlier: 3.557A  pdb=" N   VAL C  32 " --> pdb=" O   ASP C  28 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 67 through 102
    Processing helix  chain 'C' and resid 103 through 105
      No H-bonds generated for 'chain 'C' and resid 103 through 105'
    Processing helix  chain 'C' and resid 114 through 142
      removed outlier: 3.654A  pdb=" N   SER C 129 " --> pdb=" O   PHE C 125 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   ASN C 136 " --> pdb=" O   PHE C 132 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   ILE C 137 " --> pdb=" O   SER C 133 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   ALA C 139 " --> pdb=" O   ILE C 135 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 155 through 185
      removed outlier: 3.510A  pdb=" N   PHE C 179 " --> pdb=" O   GLY C 175 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   ASP C 180 " --> pdb=" O   VAL C 176 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 186 through 206
      removed outlier: 3.939A  pdb=" N   LEU C 190 " --> pdb=" O   ARG C 186 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 213 through 233
      removed outlier: 3.759A  pdb=" N   ILE C 217 " --> pdb=" O   SER C 213 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 235 through 243
      removed outlier: 3.590A  pdb=" N   LEU C 243 " --> pdb=" O   ILE C 239 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 8 through 20
      removed outlier: 3.801A  pdb=" N   ASN D  13 " --> pdb=" O   GLU D   9 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 26 through 42
      removed outlier: 3.782A  pdb=" N   TRP D  30 " --> pdb=" O   LEU D  26 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   TRP D  36 " --> pdb=" O   VAL D  32 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 49 through 54
    Processing helix  chain 'D' and resid 55 through 82
    Processing helix  chain 'D' and resid 86 through 92
    Processing sheet with id=AA, first strand: chain 'A' and resid 42 through 43
      removed outlier: 6.559A  pdb=" N   CYS A 213 " --> pdb=" O   ILE A  73 " (cutoff:3.500A)
    Processing sheet with id=AB, first strand: chain 'A' and resid 59 through 60
    Processing sheet with id=AC, first strand: chain 'A' and resid 413 through 414
      removed outlier: 3.543A  pdb=" N   VAL A 440 " --> pdb=" O   HIS A 379 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   SER A 437 " --> pdb=" O   PHE A 362 " (cutoff:3.500A)
    Processing sheet with id=AD, first strand: chain 'A' and resid 413 through 414
      removed outlier: 3.543A  pdb=" N   VAL A 440 " --> pdb=" O   HIS A 379 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   SER A 361 " --> pdb=" O   VAL A 275 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   TRP A 257 " --> pdb=" O   ARG A 626 " (cutoff:3.500A)
    Processing sheet with id=AE, first strand: chain 'A' and resid 437 through 438
      removed outlier: 6.800A  pdb=" N   SER A 437 " --> pdb=" O   PHE A 362 " (cutoff:3.500A)
    Processing sheet with id=AF, first strand: chain 'A' and resid 603 through 604
    Processing sheet with id=BA, first strand: chain 'B' and resid 193 through 194
      removed outlier: 6.969A  pdb=" N   VAL B 193 " --> pdb=" O   PHE D  94 " (cutoff:3.500A)

    572 hydrogen bonds defined for protein.
    1671 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.71

  Time building geometry restraints manager: 1.20 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1599
        1.32 -     1.45: 2853
        1.45 -     1.58: 5376
        1.58 -     1.71: 12
        1.71 -     1.83: 54
  Bond restraints: 9894
  Sorted by residual:
  bond pdb=" CA  SER B 401 "
       pdb=" C   SER B 401 "
    ideal  model  delta    sigma   weight residual
    1.523  1.608 -0.084 1.34e-02 5.57e+03 3.97e+01
  bond pdb=" N   LEU C 243 "
       pdb=" CA  LEU C 243 "
    ideal  model  delta    sigma   weight residual
    1.457  1.528 -0.070 1.29e-02 6.01e+03 2.98e+01
  bond pdb=" CA  VAL A 579 "
       pdb=" C   VAL A 579 "
    ideal  model  delta    sigma   weight residual
    1.520  1.578 -0.058 1.07e-02 8.73e+03 2.95e+01
  bond pdb=" CA  LEU B 452 "
       pdb=" C   LEU B 452 "
    ideal  model  delta    sigma   weight residual
    1.525  1.476  0.050 1.02e-02 9.61e+03 2.37e+01
  bond pdb=" CA  LEU C 243 "
       pdb=" C   LEU C 243 "
    ideal  model  delta    sigma   weight residual
    1.523  1.582 -0.059 1.34e-02 5.57e+03 1.95e+01
  ... (remaining 9889 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.57: 11297
        2.57 -     5.15: 1993
        5.15 -     7.72: 166
        7.72 -    10.30: 23
       10.30 -    12.87: 9
  Bond angle restraints: 13488
  Sorted by residual:
  angle pdb=" N   VAL C 120 "
        pdb=" CA  VAL C 120 "
        pdb=" CB  VAL C 120 "
      ideal   model   delta    sigma   weight residual
     110.55  119.51   -8.96 1.17e+00 7.31e-01 5.87e+01
  angle pdb=" N   GLY A 547 "
        pdb=" CA  GLY A 547 "
        pdb=" C   GLY A 547 "
      ideal   model   delta    sigma   weight residual
     112.57  102.37   10.20 1.37e+00 5.33e-01 5.54e+01
  angle pdb=" N   ALA B 400 "
        pdb=" CA  ALA B 400 "
        pdb=" C   ALA B 400 "
      ideal   model   delta    sigma   weight residual
     109.40  121.49  -12.09 1.63e+00 3.76e-01 5.50e+01
  angle pdb=" CA  PHE C  88 "
        pdb=" C   PHE C  88 "
        pdb=" N   ALA C  89 "
      ideal   model   delta    sigma   weight residual
     117.07  108.95    8.12 1.14e+00 7.69e-01 5.07e+01
  angle pdb=" C   ILE B 387 "
        pdb=" CA  ILE B 387 "
        pdb=" CB  ILE B 387 "
      ideal   model   delta    sigma   weight residual
     111.97  102.87    9.10 1.28e+00 6.10e-01 5.06e+01
  ... (remaining 13483 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.40: 4792
       17.40 -    34.79: 691
       34.79 -    52.19: 221
       52.19 -    69.59: 57
       69.59 -    86.99: 10
  Dihedral angle restraints: 5771
    sinusoidal: 2196
      harmonic: 3575
  Sorted by residual:
  dihedral pdb=" CA  ALA B 400 "
           pdb=" C   ALA B 400 "
           pdb=" N   SER B 401 "
           pdb=" CA  SER B 401 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -128.06  -51.94     0      5.00e+00 4.00e-02 1.08e+02
  dihedral pdb=" CB  CYS A 230 "
           pdb=" SG  CYS A 230 "
           pdb=" SG  CYS A 248 "
           pdb=" CB  CYS A 248 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  179.99  -86.99     1      1.00e+01 1.00e-02 9.10e+01
  dihedral pdb=" CA  TYR B 106 "
           pdb=" C   TYR B 106 "
           pdb=" N   THR B 107 "
           pdb=" CA  THR B 107 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  132.58   47.42     0      5.00e+00 4.00e-02 8.99e+01
  ... (remaining 5768 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.151: 1341
       0.151 -    0.301: 185
       0.301 -    0.452: 26
       0.452 -    0.602: 6
       0.602 -    0.753: 2
  Chirality restraints: 1560
  Sorted by residual:
  chirality pdb=" CA  PHE A 218 "
            pdb=" N   PHE A 218 "
            pdb=" C   PHE A 218 "
            pdb=" CB  PHE A 218 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.76    0.75 2.00e-01 2.50e+01 1.42e+01
  chirality pdb=" CA  PHE A 302 "
            pdb=" N   PHE A 302 "
            pdb=" C   PHE A 302 "
            pdb=" CB  PHE A 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.78    0.73 2.00e-01 2.50e+01 1.33e+01
  chirality pdb=" CA  TYR B 225 "
            pdb=" N   TYR B 225 "
            pdb=" C   TYR B 225 "
            pdb=" CB  TYR B 225 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.93    0.58 2.00e-01 2.50e+01 8.45e+00
  ... (remaining 1557 not shown)

  Planarity restraints: 1680
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 559 "    0.072 5.00e-02 4.00e+02   1.10e-01 1.92e+01
        pdb=" N   PRO A 560 "   -0.190 5.00e-02 4.00e+02
        pdb=" CA  PRO A 560 "    0.062 5.00e-02 4.00e+02
        pdb=" CD  PRO A 560 "    0.056 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B  87 "    0.064 5.00e-02 4.00e+02   9.62e-02 1.48e+01
        pdb=" N   PRO B  88 "   -0.166 5.00e-02 4.00e+02
        pdb=" CA  PRO B  88 "    0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO B  88 "    0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 388 "    0.038 2.00e-02 2.50e+03   2.64e-02 1.22e+01
        pdb=" CG  PHE B 388 "   -0.056 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 388 "    0.000 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 388 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 388 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 388 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 388 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1677 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 132
        2.64 -     3.20: 9550
        3.20 -     3.77: 16000
        3.77 -     4.33: 20541
        4.33 -     4.90: 33144
  Nonbonded interactions: 79367
  Sorted by model distance:
  nonbonded pdb=" O   ILE C  34 "
            pdb=" OH  TYR C  90 "
     model   vdw
     2.074 3.040
  nonbonded pdb=" O   ALA B 396 "
            pdb=" OG1 THR B 399 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" O   LEU A 397 "
            pdb=" OG1 THR A 400 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" O   LEU C  35 "
            pdb=" OG  SER C 124 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" O   ALA C  76 "
            pdb=" OG  SER C  79 "
     model   vdw
     2.280 3.040
  ... (remaining 79362 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.420
  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:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.750
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6489
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      :  0.012   0.095   9899  Z= 0.785
  Angle     :  1.850  12.870  13498  Z= 1.291
  Chirality :  0.113   0.753   1560
  Planarity :  0.008   0.110   1680
  Dihedral  : 18.823  81.957   3448
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 13.59
  Ramachandran Plot:
    Outliers :  4.30 %
    Allowed  : 11.41 %
    Favored  : 84.28 %
  Rotamer:
    Outliers : 14.00 %
    Allowed  : 16.49 %
    Favored  : 69.51 %
  Cbeta Deviations :  2.43 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 1.85 %
    Twisted General : 1.29 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.91 (0.22), residues: 1209
  helix:  1.07 (0.16), residues: 660
  sheet: -3.39 (0.45), residues: 100
  loop : -4.58 (0.22), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 657 
 TYR   0.042   0.004   TYR B 225 
 PHE   0.059   0.005   PHE A 302 
 TRP   0.031   0.004   TRP D  36 
 HIS   0.013   0.003   HIS A  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.01201 ( 9894)
  covalent geometry    : angle       1.85036 (13488)
  SS BOND              : bond        0.01809 (    5)
  SS BOND              : angle       1.98811 (   10)
  hydrogen bonds       : bond        0.15835 (  564)
  hydrogen bonds       : angle       6.24010 ( 1671)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  386 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 146
    poor density    : 240
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 MET cc_start: 0.9170 (mmt) cc_final: 0.8794 (mmm)
REVERT: A  129 SER cc_start: 0.7373 (OUTLIER) cc_final: 0.6535 (t)
REVERT: A  333 GLU cc_start: 0.9323 (OUTLIER) cc_final: 0.8792 (mp0)
REVERT: A  349 LYS cc_start: 0.9546 (mmtt) cc_final: 0.9223 (mppt)
REVERT: A  378 MET cc_start: 0.9135 (mpt) cc_final: 0.8745 (mpp)
REVERT: A  425 SER cc_start: 0.8302 (OUTLIER) cc_final: 0.7908 (t)
REVERT: A  426 SER cc_start: 0.9586 (t) cc_final: 0.8770 (p)
REVERT: A  430 PHE cc_start: 0.9607 (m-80) cc_final: 0.9003 (m-80)
REVERT: A  512 GLN cc_start: 0.9340 (OUTLIER) cc_final: 0.8960 (pp30)
REVERT: A  522 LEU cc_start: 0.9666 (OUTLIER) cc_final: 0.9450 (mt)
REVERT: A  555 ILE cc_start: 0.7981 (mt) cc_final: 0.6548 (mt)
REVERT: A  574 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8841 (mt)
REVERT: A  624 THR cc_start: 0.7194 (OUTLIER) cc_final: 0.6822 (m)
REVERT: A  644 GLU cc_start: 0.9115 (OUTLIER) cc_final: 0.8894 (pp20)
REVERT: A  655 ASP cc_start: 0.8547 (m-30) cc_final: 0.8202 (p0)
REVERT: B   80 LYS cc_start: 0.9357 (tttt) cc_final: 0.8991 (mttm)
REVERT: B  105 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8563 (t80)
REVERT: B  184 GLU cc_start: 0.9375 (OUTLIER) cc_final: 0.9130 (mm-30)
REVERT: B  194 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8144 (p0)
REVERT: B  195 TYR cc_start: 0.8934 (OUTLIER) cc_final: 0.8652 (m-80)
REVERT: B  386 PHE cc_start: 0.8150 (t80) cc_final: 0.7820 (t80)
REVERT: B  405 ASN cc_start: 0.8830 (t0) cc_final: 0.8516 (t0)
REVERT: B  438 SER cc_start: 0.8016 (OUTLIER) cc_final: 0.7749 (p)
REVERT: C    9 CYS cc_start: 0.8973 (m) cc_final: 0.8604 (p)
REVERT: C   83 GLN cc_start: 0.9499 (mt0) cc_final: 0.9289 (mp10)
REVERT: C   84 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8622 (mm-30)
REVERT: C  132 PHE cc_start: 0.9522 (m-10) cc_final: 0.9305 (m-10)
REVERT: C  136 ASN cc_start: 0.9112 (m-40) cc_final: 0.8752 (p0)
REVERT: C  140 ASP cc_start: 0.8118 (m-30) cc_final: 0.7765 (m-30)
REVERT: D    5 ARG cc_start: 0.8240 (mtm180) cc_final: 0.8029 (ptt90)
REVERT: D   28 PHE cc_start: 0.9231 (t80) cc_final: 0.8868 (t80)
REVERT: D   84 ARG cc_start: 0.9253 (mtt180) cc_final: 0.9022 (mpt-90)
  outliers start: 146
  outliers final: 48
  residues processed: 346
  average time/residue: 0.0945
  time to fit residues: 46.5680
Evaluate side-chains
  222 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 161
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    7.9990
   chunk 113 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.1980
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 117 optimal weight:    6.9990
   overall best weight:    2.0388

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

Flipped N/Q/H residues before XYZ refinement:
A 142 ASN
A 237 GLN
** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 516 GLN
A 535 GLN
** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 223 GLN
C 171 HIS
** D   8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.053850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.046031 restraints weight = 68004.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.047092 restraints weight = 44535.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.047931 restraints weight = 32269.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.048485 restraints weight = 25554.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.048875 restraints weight = 21345.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.4120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   9899  Z= 0.198
  Angle     :  0.881  11.409  13498  Z= 0.458
  Chirality :  0.048   0.212   1560
  Planarity :  0.006   0.093   1680
  Dihedral  :  7.201  36.108   1319
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 16.92
  Ramachandran Plot:
    Outliers :  1.08 %
    Allowed  :  8.44 %
    Favored  : 90.49 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  :  4.12 %
    Favored  : 95.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 3.70 %
    Twisted General : 0.17 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.59 (0.25), residues: 1209
  helix:  1.91 (0.20), residues: 690
  sheet: -3.15 (0.42), residues: 114
  loop : -3.87 (0.25), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 285 
 TYR   0.023   0.002   TYR C  69 
 PHE   0.037   0.003   PHE A 302 
 TRP   0.018   0.002   TRP A 257 
 HIS   0.009   0.002   HIS A 553 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 9894)
  covalent geometry    : angle       0.87831 (13488)
  SS BOND              : bond        0.01094 (    5)
  SS BOND              : angle       2.81006 (   10)
  hydrogen bonds       : bond        0.05463 (  564)
  hydrogen bonds       : angle       5.32109 ( 1671)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 222
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 ASP cc_start: 0.8266 (m-30) cc_final: 0.7851 (m-30)
REVERT: A   95 MET cc_start: 0.8619 (mmt) cc_final: 0.8063 (mmt)
REVERT: A  195 CYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7802 (t)
REVERT: A  251 LEU cc_start: 0.9383 (mt) cc_final: 0.9077 (mt)
REVERT: A  305 GLN cc_start: 0.9441 (tp-100) cc_final: 0.9207 (tp40)
REVERT: A  349 LYS cc_start: 0.9470 (mmtt) cc_final: 0.9145 (mmtp)
REVERT: A  430 PHE cc_start: 0.8964 (m-80) cc_final: 0.8722 (m-80)
REVERT: A  457 TYR cc_start: 0.8319 (m-80) cc_final: 0.7813 (m-80)
REVERT: A  538 LEU cc_start: 0.9384 (mt) cc_final: 0.9067 (mt)
REVERT: A  553 HIS cc_start: 0.9025 (m-70) cc_final: 0.8818 (m90)
REVERT: A  640 TRP cc_start: 0.8834 (m-10) cc_final: 0.8633 (m-10)
REVERT: A  655 ASP cc_start: 0.8727 (m-30) cc_final: 0.8381 (p0)
REVERT: A  657 ARG cc_start: 0.9071 (ptt-90) cc_final: 0.8647 (ptt90)
REVERT: B  103 VAL cc_start: 0.9342 (t) cc_final: 0.8911 (t)
REVERT: B  171 LEU cc_start: 0.9800 (tt) cc_final: 0.9591 (tp)
REVERT: B  184 GLU cc_start: 0.9139 (mm-30) cc_final: 0.8682 (mm-30)
REVERT: B  194 ASP cc_start: 0.9086 (p0) cc_final: 0.8341 (p0)
REVERT: B  225 TYR cc_start: 0.8775 (m-10) cc_final: 0.8354 (m-80)
REVERT: B  457 MET cc_start: 0.9541 (mmp) cc_final: 0.9191 (ptt)
REVERT: C   86 PHE cc_start: 0.9132 (m-10) cc_final: 0.8796 (m-10)
REVERT: C  109 ARG cc_start: 0.8194 (pmt-80) cc_final: 0.7969 (ptm-80)
REVERT: C  135 ILE cc_start: 0.9245 (tp) cc_final: 0.8945 (tp)
REVERT: C  140 ASP cc_start: 0.8666 (m-30) cc_final: 0.8387 (m-30)
REVERT: C  197 HIS cc_start: 0.9679 (t-170) cc_final: 0.9132 (t-170)
REVERT: D   28 PHE cc_start: 0.9093 (t80) cc_final: 0.8843 (t80)
REVERT: D   69 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8886 (tp)
  outliers start: 7
  outliers final: 0
  residues processed: 226
  average time/residue: 0.0834
  time to fit residues: 27.5464
Evaluate side-chains
  153 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 151
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 108 optimal weight:    0.3980
   chunk 10 optimal weight:    4.9990
   chunk 43 optimal weight:    8.9990
   chunk 107 optimal weight:   10.0000
   chunk 58 optimal weight:    6.9990
   chunk 116 optimal weight:    0.4980
   chunk 110 optimal weight:   10.0000
   chunk 18 optimal weight:   10.0000
   chunk 114 optimal weight:    9.9990
   chunk 120 optimal weight:   10.0000
   overall best weight:    2.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 420 GLN
** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 222 GLN ** 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 = 0.3213 r_free = 0.3213 target = 0.052253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.044960 restraints weight = 72432.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.046028 restraints weight = 46614.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.046836 restraints weight = 33404.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.047330 restraints weight = 26312.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.047703 restraints weight = 21989.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.4915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.073   9899  Z= 0.188
  Angle     :  0.782  11.134  13498  Z= 0.405
  Chirality :  0.045   0.204   1560
  Planarity :  0.006   0.100   1680
  Dihedral  :  6.512  33.945   1319
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 16.45
  Ramachandran Plot:
    Outliers :  0.91 %
    Allowed  :  8.44 %
    Favored  : 90.65 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  4.99 %
    Favored  : 94.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 1.85 %
    Twisted General : 0.17 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.70 (0.24), residues: 1209
  helix:  1.48 (0.19), residues: 690
  sheet: -2.45 (0.46), residues: 104
  loop : -3.46 (0.27), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 184 
 TYR   0.023   0.002   TYR B 446 
 PHE   0.034   0.002   PHE A 302 
 TRP   0.018   0.001   TRP D  67 
 HIS   0.007   0.002   HIS A 553 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 9894)
  covalent geometry    : angle       0.77952 (13488)
  SS BOND              : bond        0.01295 (    5)
  SS BOND              : angle       2.43991 (   10)
  hydrogen bonds       : bond        0.04796 (  564)
  hydrogen bonds       : angle       4.97813 ( 1671)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 199
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 VAL cc_start: 0.7924 (OUTLIER) cc_final: 0.7513 (m)
REVERT: A  231 MET cc_start: 0.9522 (ttt) cc_final: 0.9214 (ttm)
REVERT: A  251 LEU cc_start: 0.9368 (mt) cc_final: 0.9042 (mt)
REVERT: A  305 GLN cc_start: 0.9403 (tp-100) cc_final: 0.9178 (tp40)
REVERT: A  347 MET cc_start: 0.9176 (mmp) cc_final: 0.8668 (tpp)
REVERT: A  457 TYR cc_start: 0.8448 (m-80) cc_final: 0.7983 (m-80)
REVERT: A  538 LEU cc_start: 0.9496 (mt) cc_final: 0.9172 (mt)
REVERT: A  684 LEU cc_start: 0.9473 (mm) cc_final: 0.9254 (mm)
REVERT: B   92 CYS cc_start: 0.8896 (t) cc_final: 0.8694 (p)
REVERT: B  184 GLU cc_start: 0.9381 (mm-30) cc_final: 0.8887 (mm-30)
REVERT: B  194 ASP cc_start: 0.9074 (p0) cc_final: 0.8518 (p0)
REVERT: B  225 TYR cc_start: 0.8814 (m-10) cc_final: 0.8574 (m-80)
REVERT: B  233 MET cc_start: 0.9009 (tpt) cc_final: 0.8766 (tpp)
REVERT: B  239 LYS cc_start: 0.9192 (tmmt) cc_final: 0.8888 (ttpp)
REVERT: B  386 PHE cc_start: 0.8857 (t80) cc_final: 0.7986 (t80)
REVERT: B  391 VAL cc_start: 0.9503 (t) cc_final: 0.9245 (t)
REVERT: B  457 MET cc_start: 0.9704 (mmp) cc_final: 0.9426 (mmm)
REVERT: C   35 LEU cc_start: 0.9779 (tt) cc_final: 0.9556 (mm)
REVERT: C   86 PHE cc_start: 0.9181 (m-10) cc_final: 0.8893 (m-10)
REVERT: C   90 TYR cc_start: 0.8791 (t80) cc_final: 0.8467 (t80)
REVERT: C   98 ASP cc_start: 0.9544 (t0) cc_final: 0.9202 (m-30)
REVERT: C   99 GLU cc_start: 0.8145 (pt0) cc_final: 0.7851 (pp20)
REVERT: C  109 ARG cc_start: 0.8294 (pmt-80) cc_final: 0.7715 (ptm-80)
REVERT: C  132 PHE cc_start: 0.9479 (m-10) cc_final: 0.9197 (m-10)
REVERT: C  140 ASP cc_start: 0.8742 (m-30) cc_final: 0.8484 (m-30)
REVERT: C  197 HIS cc_start: 0.9605 (t-170) cc_final: 0.9300 (t-170)
REVERT: D   69 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.8931 (tp)
  outliers start: 3
  outliers final: 0
  residues processed: 202
  average time/residue: 0.0882
  time to fit residues: 26.0985
Evaluate side-chains
  152 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 150
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 92 optimal weight:   10.0000
   chunk 49 optimal weight:    9.9990
   chunk 70 optimal weight:    9.9990
   chunk 100 optimal weight:    1.9990
   chunk 26 optimal weight:    6.9990
   chunk 1 optimal weight:   20.0000
   chunk 78 optimal weight:    0.9990
   chunk 73 optimal weight:    8.9990
   chunk 58 optimal weight:   20.0000
   chunk 48 optimal weight:    2.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 553 HIS
A 562 ASN
** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.051290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.044011 restraints weight = 76033.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.044989 restraints weight = 49152.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.045776 restraints weight = 35808.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.046273 restraints weight = 28318.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.046661 restraints weight = 23559.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.5461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   9899  Z= 0.185
  Angle     :  0.762  11.278  13498  Z= 0.396
  Chirality :  0.044   0.200   1560
  Planarity :  0.006   0.089   1680
  Dihedral  :  6.187  34.991   1319
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 17.90
  Ramachandran Plot:
    Outliers :  0.99 %
    Allowed  :  8.02 %
    Favored  : 90.98 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  4.41 %
    Favored  : 95.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 1.85 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.67 (0.24), residues: 1209
  helix:  1.34 (0.19), residues: 696
  sheet: -2.36 (0.44), residues: 114
  loop : -3.22 (0.29), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 117 
 TYR   0.019   0.002   TYR B 106 
 PHE   0.032   0.002   PHE A 302 
 TRP   0.018   0.001   TRP D  67 
 HIS   0.007   0.001   HIS C  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 9894)
  covalent geometry    : angle       0.75502 (13488)
  SS BOND              : bond        0.00829 (    5)
  SS BOND              : angle       3.92191 (   10)
  hydrogen bonds       : bond        0.04614 (  564)
  hydrogen bonds       : angle       4.83736 ( 1671)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 192
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  182 LEU cc_start: 0.9625 (tp) cc_final: 0.9270 (pp)
REVERT: A  231 MET cc_start: 0.9527 (ttt) cc_final: 0.9220 (ttm)
REVERT: A  330 PHE cc_start: 0.8892 (m-80) cc_final: 0.8569 (m-80)
REVERT: A  347 MET cc_start: 0.9139 (mmp) cc_final: 0.8833 (mmp)
REVERT: A  457 TYR cc_start: 0.8209 (m-80) cc_final: 0.7741 (m-80)
REVERT: A  538 LEU cc_start: 0.9418 (mt) cc_final: 0.9051 (mt)
REVERT: A  554 TYR cc_start: 0.8902 (t80) cc_final: 0.8664 (t80)
REVERT: B   80 LYS cc_start: 0.9323 (tttt) cc_final: 0.9025 (mttt)
REVERT: B  103 VAL cc_start: 0.9489 (t) cc_final: 0.9252 (t)
REVERT: B  184 GLU cc_start: 0.9353 (mm-30) cc_final: 0.8999 (mm-30)
REVERT: B  194 ASP cc_start: 0.9098 (p0) cc_final: 0.8348 (p0)
REVERT: B  195 TYR cc_start: 0.9035 (m-10) cc_final: 0.8701 (m-10)
REVERT: B  221 LEU cc_start: 0.8713 (mt) cc_final: 0.7816 (mt)
REVERT: B  225 TYR cc_start: 0.8703 (m-10) cc_final: 0.8498 (m-10)
REVERT: B  233 MET cc_start: 0.9166 (tpt) cc_final: 0.8892 (tpp)
REVERT: B  441 PHE cc_start: 0.9488 (m-80) cc_final: 0.8729 (m-80)
REVERT: B  450 ASP cc_start: 0.9082 (t0) cc_final: 0.8706 (p0)
REVERT: B  457 MET cc_start: 0.9543 (mmp) cc_final: 0.9339 (mmp)
REVERT: C   35 LEU cc_start: 0.9772 (tt) cc_final: 0.9567 (mm)
REVERT: C   84 GLU cc_start: 0.9377 (pp20) cc_final: 0.9046 (pp20)
REVERT: C   86 PHE cc_start: 0.9204 (m-10) cc_final: 0.8891 (m-10)
REVERT: C   98 ASP cc_start: 0.9483 (t0) cc_final: 0.9219 (m-30)
REVERT: C  109 ARG cc_start: 0.8184 (pmt-80) cc_final: 0.7678 (ptm-80)
REVERT: C  132 PHE cc_start: 0.9557 (m-10) cc_final: 0.9213 (m-10)
REVERT: C  199 LEU cc_start: 0.9285 (mm) cc_final: 0.9080 (pp)
REVERT: C  218 TYR cc_start: 0.9344 (m-80) cc_final: 0.9060 (m-80)
REVERT: D   69 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.8979 (tp)
  outliers start: 3
  outliers final: 2
  residues processed: 193
  average time/residue: 0.0836
  time to fit residues: 24.1880
Evaluate side-chains
  145 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 142
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 70 optimal weight:    7.9990
   chunk 119 optimal weight:    7.9990
   chunk 5 optimal weight:   30.0000
   chunk 111 optimal weight:   30.0000
   chunk 14 optimal weight:    5.9990
   chunk 61 optimal weight:    9.9990
   chunk 44 optimal weight:    9.9990
   chunk 81 optimal weight:    0.7980
   chunk 106 optimal weight:   10.0000
   chunk 71 optimal weight:    8.9990
   chunk 45 optimal weight:   10.0000
   overall best weight:    6.3588

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

Flipped N/Q/H residues before XYZ refinement:
** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 379 HIS
A 449 HIS
** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 606 GLN
** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 207 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.047996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.041114 restraints weight = 78804.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.042056 restraints weight = 51288.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.042770 restraints weight = 37607.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.043268 restraints weight = 29763.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.043561 restraints weight = 24820.162|
|-----------------------------------------------------------------------------|
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.5804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.074   9899  Z= 0.298
  Angle     :  0.842  11.272  13498  Z= 0.437
  Chirality :  0.046   0.241   1560
  Planarity :  0.007   0.085   1680
  Dihedral  :  6.423  30.732   1319
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 23.82
  Ramachandran Plot:
    Outliers :  0.91 %
    Allowed  :  8.93 %
    Favored  : 90.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 1.85 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.08 (0.24), residues: 1209
  helix:  0.95 (0.19), residues: 686
  sheet: -2.51 (0.45), residues: 111
  loop : -3.17 (0.28), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 117 
 TYR   0.020   0.002   TYR B 106 
 PHE   0.033   0.003   PHE A 302 
 TRP   0.029   0.002   TRP B 244 
 HIS   0.011   0.003   HIS C 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00620 ( 9894)
  covalent geometry    : angle       0.83871 (13488)
  SS BOND              : bond        0.01078 (    5)
  SS BOND              : angle       2.84099 (   10)
  hydrogen bonds       : bond        0.04892 (  564)
  hydrogen bonds       : angle       5.06184 ( 1671)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 MET cc_start: 0.8416 (mpp) cc_final: 0.7872 (mpp)
REVERT: A  182 LEU cc_start: 0.9677 (tp) cc_final: 0.9252 (pp)
REVERT: A  213 CYS cc_start: 0.5068 (t) cc_final: 0.4843 (t)
REVERT: A  231 MET cc_start: 0.9490 (ttt) cc_final: 0.9104 (ttm)
REVERT: A  347 MET cc_start: 0.9138 (mmp) cc_final: 0.8788 (mmp)
REVERT: A  378 MET cc_start: 0.8771 (mpp) cc_final: 0.8568 (mpp)
REVERT: A  538 LEU cc_start: 0.9437 (mt) cc_final: 0.9008 (mt)
REVERT: A  553 HIS cc_start: 0.8674 (m90) cc_final: 0.8452 (m90)
REVERT: A  655 ASP cc_start: 0.8307 (m-30) cc_final: 0.8033 (p0)
REVERT: A  657 ARG cc_start: 0.8926 (ptt-90) cc_final: 0.8096 (ptt90)
REVERT: A  677 PHE cc_start: 0.9355 (m-80) cc_final: 0.8969 (m-80)
REVERT: B   92 CYS cc_start: 0.8442 (t) cc_final: 0.8192 (t)
REVERT: B  103 VAL cc_start: 0.9525 (t) cc_final: 0.9271 (t)
REVERT: B  184 GLU cc_start: 0.9331 (mm-30) cc_final: 0.8795 (mm-30)
REVERT: B  186 PHE cc_start: 0.9059 (m-10) cc_final: 0.8825 (m-80)
REVERT: B  195 TYR cc_start: 0.9005 (m-10) cc_final: 0.8639 (m-80)
REVERT: B  225 TYR cc_start: 0.8891 (m-10) cc_final: 0.8558 (m-80)
REVERT: B  386 PHE cc_start: 0.8615 (t80) cc_final: 0.8391 (t80)
REVERT: B  457 MET cc_start: 0.9607 (mmp) cc_final: 0.9392 (mmp)
REVERT: B  459 GLN cc_start: 0.9282 (tp40) cc_final: 0.8923 (tp40)
REVERT: C   84 GLU cc_start: 0.9398 (pp20) cc_final: 0.9077 (pp20)
REVERT: C   86 PHE cc_start: 0.9195 (m-10) cc_final: 0.8837 (m-10)
REVERT: C   99 GLU cc_start: 0.8615 (pt0) cc_final: 0.8294 (pp20)
REVERT: C  119 TYR cc_start: 0.9231 (t80) cc_final: 0.8920 (t80)
REVERT: C  132 PHE cc_start: 0.9395 (m-10) cc_final: 0.9132 (m-10)
REVERT: C  218 TYR cc_start: 0.9415 (m-80) cc_final: 0.8980 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.0840
  time to fit residues: 21.3066
Evaluate side-chains
  130 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 57 optimal weight:    4.9990
   chunk 75 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   chunk 46 optimal weight:    4.9990
   chunk 31 optimal weight:    4.9990
   chunk 37 optimal weight:    0.0570
   chunk 49 optimal weight:    3.9990
   chunk 101 optimal weight:    2.9990
   chunk 78 optimal weight:    5.9990
   chunk 1 optimal weight:   20.0000
   overall best weight:    3.0106

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

Flipped N/Q/H residues before XYZ refinement:
A 367 GLN
** A 450 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 = 0.3155 r_free = 0.3155 target = 0.049317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.042212 restraints weight = 75459.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.043213 restraints weight = 49066.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.043939 restraints weight = 36022.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.044458 restraints weight = 28449.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.044824 restraints weight = 23582.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.6129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   9899  Z= 0.183
  Angle     :  0.758  11.607  13498  Z= 0.390
  Chirality :  0.044   0.190   1560
  Planarity :  0.006   0.089   1680
  Dihedral  :  6.066  31.683   1319
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 19.56
  Ramachandran Plot:
    Outliers :  0.83 %
    Allowed  :  7.53 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 1.85 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.87 (0.24), residues: 1209
  helix:  1.08 (0.19), residues: 695
  sheet: -2.20 (0.48), residues: 108
  loop : -3.16 (0.28), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 117 
 TYR   0.019   0.002   TYR C  90 
 PHE   0.031   0.002   PHE A 302 
 TRP   0.018   0.002   TRP B 244 
 HIS   0.006   0.002   HIS C 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 9894)
  covalent geometry    : angle       0.75428 (13488)
  SS BOND              : bond        0.01418 (    5)
  SS BOND              : angle       2.74775 (   10)
  hydrogen bonds       : bond        0.04618 (  564)
  hydrogen bonds       : angle       4.90976 ( 1671)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  182 LEU cc_start: 0.9661 (tp) cc_final: 0.9284 (pp)
REVERT: A  213 CYS cc_start: 0.4884 (t) cc_final: 0.4365 (t)
REVERT: A  231 MET cc_start: 0.9521 (ttt) cc_final: 0.9062 (ttm)
REVERT: A  347 MET cc_start: 0.9109 (mmp) cc_final: 0.8602 (mmp)
REVERT: A  554 TYR cc_start: 0.8906 (t80) cc_final: 0.8664 (t80)
REVERT: B   92 CYS cc_start: 0.8527 (t) cc_final: 0.8109 (t)
REVERT: B  103 VAL cc_start: 0.9468 (t) cc_final: 0.9234 (t)
REVERT: B  184 GLU cc_start: 0.9362 (mm-30) cc_final: 0.8935 (mm-30)
REVERT: B  195 TYR cc_start: 0.9044 (m-10) cc_final: 0.8526 (m-80)
REVERT: B  221 LEU cc_start: 0.8668 (mt) cc_final: 0.7665 (mt)
REVERT: B  225 TYR cc_start: 0.8847 (m-10) cc_final: 0.8553 (m-80)
REVERT: B  228 MET cc_start: 0.9448 (mpp) cc_final: 0.9247 (mmt)
REVERT: B  233 MET cc_start: 0.9261 (mmp) cc_final: 0.8956 (tpt)
REVERT: B  386 PHE cc_start: 0.8500 (t80) cc_final: 0.8126 (t80)
REVERT: B  457 MET cc_start: 0.9617 (mmp) cc_final: 0.9395 (mmp)
REVERT: B  459 GLN cc_start: 0.9288 (tp40) cc_final: 0.8957 (tp40)
REVERT: C    9 CYS cc_start: 0.9647 (m) cc_final: 0.9128 (p)
REVERT: C   35 LEU cc_start: 0.9483 (mm) cc_final: 0.9246 (mm)
REVERT: C   53 TRP cc_start: 0.9015 (t60) cc_final: 0.8635 (t60)
REVERT: C   84 GLU cc_start: 0.9352 (pp20) cc_final: 0.9053 (pp20)
REVERT: C   86 PHE cc_start: 0.9132 (m-10) cc_final: 0.8835 (m-10)
REVERT: C   98 ASP cc_start: 0.9408 (t0) cc_final: 0.9140 (m-30)
REVERT: C   99 GLU cc_start: 0.8512 (pt0) cc_final: 0.8149 (pp20)
REVERT: C  119 TYR cc_start: 0.9115 (t80) cc_final: 0.8880 (t80)
REVERT: C  132 PHE cc_start: 0.9351 (m-10) cc_final: 0.9145 (m-10)
REVERT: C  218 TYR cc_start: 0.9382 (m-80) cc_final: 0.8908 (m-80)
REVERT: D   32 VAL cc_start: 0.9221 (t) cc_final: 0.8983 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.0830
  time to fit residues: 21.0101
Evaluate side-chains
  134 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 112 optimal weight:   20.0000
   chunk 24 optimal weight:    0.8980
   chunk 98 optimal weight:   30.0000
   chunk 92 optimal weight:    8.9990
   chunk 42 optimal weight:    6.9990
   chunk 72 optimal weight:   10.0000
   chunk 34 optimal weight:    5.9990
   chunk 82 optimal weight:    5.9990
   chunk 84 optimal weight:   10.0000
   chunk 106 optimal weight:    4.9990
   chunk 8 optimal weight:   20.0000
   overall best weight:    4.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  79 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.047954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.041089 restraints weight = 77613.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.042018 restraints weight = 51641.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.042652 restraints weight = 38392.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.043216 restraints weight = 30117.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.043504 restraints weight = 25310.781|
|-----------------------------------------------------------------------------|
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8106
moved from start:          0.6340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   9899  Z= 0.248
  Angle     :  0.793  11.532  13498  Z= 0.412
  Chirality :  0.044   0.181   1560
  Planarity :  0.006   0.087   1680
  Dihedral  :  6.154  29.551   1319
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 22.73
  Ramachandran Plot:
    Outliers :  0.83 %
    Allowed  :  8.85 %
    Favored  : 90.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.03 (0.24), residues: 1209
  helix:  0.93 (0.19), residues: 688
  sheet: -2.30 (0.47), residues: 113
  loop : -3.10 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 117 
 TYR   0.024   0.002   TYR C  90 
 PHE   0.031   0.002   PHE A 302 
 TRP   0.032   0.002   TRP B 404 
 HIS   0.008   0.002   HIS C  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00520 ( 9894)
  covalent geometry    : angle       0.78771 (13488)
  SS BOND              : bond        0.00931 (    5)
  SS BOND              : angle       3.53010 (   10)
  hydrogen bonds       : bond        0.04695 (  564)
  hydrogen bonds       : angle       5.03904 ( 1671)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  182 LEU cc_start: 0.9546 (tp) cc_final: 0.9090 (pp)
REVERT: A  213 CYS cc_start: 0.4937 (t) cc_final: 0.4287 (t)
REVERT: A  343 MET cc_start: 0.8917 (mmp) cc_final: 0.8319 (mmm)
REVERT: A  347 MET cc_start: 0.9224 (mmp) cc_final: 0.8575 (mmp)
REVERT: A  378 MET cc_start: 0.8766 (mpp) cc_final: 0.8558 (mpp)
REVERT: A  538 LEU cc_start: 0.9434 (mt) cc_final: 0.9053 (tp)
REVERT: A  553 HIS cc_start: 0.8548 (m90) cc_final: 0.8297 (m90)
REVERT: A  554 TYR cc_start: 0.8932 (t80) cc_final: 0.8686 (t80)
REVERT: B   80 LYS cc_start: 0.9331 (tttt) cc_final: 0.9010 (mttm)
REVERT: B   92 CYS cc_start: 0.8508 (t) cc_final: 0.8127 (t)
REVERT: B  184 GLU cc_start: 0.9360 (mm-30) cc_final: 0.8993 (mm-30)
REVERT: B  195 TYR cc_start: 0.9119 (m-10) cc_final: 0.8525 (m-10)
REVERT: B  225 TYR cc_start: 0.8866 (m-10) cc_final: 0.8567 (m-80)
REVERT: B  386 PHE cc_start: 0.8589 (t80) cc_final: 0.8178 (t80)
REVERT: B  457 MET cc_start: 0.9646 (mmp) cc_final: 0.9406 (mmp)
REVERT: B  459 GLN cc_start: 0.9261 (tp40) cc_final: 0.9017 (tp40)
REVERT: C   35 LEU cc_start: 0.9554 (mm) cc_final: 0.9351 (mm)
REVERT: C   53 TRP cc_start: 0.8998 (t60) cc_final: 0.8633 (t60)
REVERT: C   84 GLU cc_start: 0.9376 (pp20) cc_final: 0.9071 (pp20)
REVERT: C   86 PHE cc_start: 0.9154 (m-10) cc_final: 0.8847 (m-10)
REVERT: C   98 ASP cc_start: 0.9468 (t0) cc_final: 0.9152 (m-30)
REVERT: C   99 GLU cc_start: 0.8492 (pt0) cc_final: 0.8115 (pp20)
REVERT: C  119 TYR cc_start: 0.9197 (t80) cc_final: 0.8918 (t80)
REVERT: C  132 PHE cc_start: 0.9314 (m-10) cc_final: 0.8976 (m-10)
REVERT: C  167 ILE cc_start: 0.9763 (tt) cc_final: 0.9366 (tt)
REVERT: C  171 HIS cc_start: 0.9536 (m90) cc_final: 0.8787 (m-70)
REVERT: C  218 TYR cc_start: 0.9447 (m-80) cc_final: 0.8956 (m-80)
REVERT: D   32 VAL cc_start: 0.9272 (t) cc_final: 0.9019 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 157
  average time/residue: 0.0838
  time to fit residues: 19.7618
Evaluate side-chains
  128 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 116 optimal weight:    8.9990
   chunk 42 optimal weight:    8.9990
   chunk 83 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9990
   chunk 98 optimal weight:   30.0000
   chunk 46 optimal weight:    6.9990
   chunk 119 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 63 optimal weight:    5.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.049776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.042813 restraints weight = 74361.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.043782 restraints weight = 48965.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.044332 restraints weight = 35923.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.044893 restraints weight = 29363.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.045228 restraints weight = 24529.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.6584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9899  Z= 0.152
  Angle     :  0.747  11.697  13498  Z= 0.381
  Chirality :  0.044   0.219   1560
  Planarity :  0.006   0.083   1680
  Dihedral  :  5.743  29.258   1319
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 16.45
  Ramachandran Plot:
    Outliers :  0.83 %
    Allowed  :  7.61 %
    Favored  : 91.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.78 (0.24), residues: 1209
  helix:  1.08 (0.19), residues: 693
  sheet: -1.94 (0.49), residues: 110
  loop : -3.02 (0.29), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  82 
 TYR   0.022   0.001   TYR A 565 
 PHE   0.030   0.002   PHE A 302 
 TRP   0.020   0.001   TRP D  67 
 HIS   0.006   0.001   HIS C 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 9894)
  covalent geometry    : angle       0.74253 (13488)
  SS BOND              : bond        0.00492 (    5)
  SS BOND              : angle       3.05945 (   10)
  hydrogen bonds       : bond        0.04332 (  564)
  hydrogen bonds       : angle       4.84743 ( 1671)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 MET cc_start: 0.8316 (mpp) cc_final: 0.7790 (mpp)
REVERT: A  182 LEU cc_start: 0.9484 (tp) cc_final: 0.9074 (pp)
REVERT: A  213 CYS cc_start: 0.4725 (t) cc_final: 0.3806 (t)
REVERT: A  221 MET cc_start: 0.8661 (mmm) cc_final: 0.8377 (mmp)
REVERT: A  231 MET cc_start: 0.9522 (ttt) cc_final: 0.9093 (ttm)
REVERT: A  330 PHE cc_start: 0.8937 (m-80) cc_final: 0.8635 (m-80)
REVERT: A  538 LEU cc_start: 0.9420 (mt) cc_final: 0.8873 (tp)
REVERT: A  553 HIS cc_start: 0.8585 (m90) cc_final: 0.8380 (m90)
REVERT: A  554 TYR cc_start: 0.8902 (t80) cc_final: 0.8632 (t80)
REVERT: A  677 PHE cc_start: 0.9073 (m-10) cc_final: 0.8629 (m-80)
REVERT: B   84 MET cc_start: 0.9263 (mtm) cc_final: 0.8947 (mmt)
REVERT: B   92 CYS cc_start: 0.8620 (t) cc_final: 0.8104 (t)
REVERT: B  103 VAL cc_start: 0.9461 (t) cc_final: 0.9231 (t)
REVERT: B  184 GLU cc_start: 0.9347 (mm-30) cc_final: 0.8983 (mm-30)
REVERT: B  195 TYR cc_start: 0.9083 (m-10) cc_final: 0.8472 (m-10)
REVERT: B  221 LEU cc_start: 0.8784 (mt) cc_final: 0.7807 (mt)
REVERT: B  225 TYR cc_start: 0.8840 (m-10) cc_final: 0.8518 (m-80)
REVERT: B  386 PHE cc_start: 0.8571 (t80) cc_final: 0.8205 (t80)
REVERT: B  457 MET cc_start: 0.9630 (mmp) cc_final: 0.9370 (mmp)
REVERT: B  459 GLN cc_start: 0.9268 (tp40) cc_final: 0.8942 (tp40)
REVERT: C    9 CYS cc_start: 0.9633 (m) cc_final: 0.9021 (p)
REVERT: C   35 LEU cc_start: 0.9588 (mm) cc_final: 0.9267 (mm)
REVERT: C   53 TRP cc_start: 0.9029 (t60) cc_final: 0.8632 (t60)
REVERT: C   84 GLU cc_start: 0.9343 (pp20) cc_final: 0.9065 (pp20)
REVERT: C   86 PHE cc_start: 0.9145 (m-10) cc_final: 0.8849 (m-10)
REVERT: C   98 ASP cc_start: 0.9488 (t0) cc_final: 0.9162 (m-30)
REVERT: C   99 GLU cc_start: 0.8347 (pt0) cc_final: 0.8075 (pp20)
REVERT: C  109 ARG cc_start: 0.8269 (pmt-80) cc_final: 0.8047 (ptm-80)
REVERT: C  119 TYR cc_start: 0.9070 (t80) cc_final: 0.8846 (t80)
REVERT: C  129 SER cc_start: 0.8805 (t) cc_final: 0.8587 (p)
REVERT: C  132 PHE cc_start: 0.9319 (m-10) cc_final: 0.9078 (m-10)
REVERT: C  167 ILE cc_start: 0.9738 (tt) cc_final: 0.9403 (tt)
REVERT: C  171 HIS cc_start: 0.9537 (m90) cc_final: 0.8669 (m90)
REVERT: C  218 TYR cc_start: 0.9452 (m-80) cc_final: 0.8893 (m-80)
REVERT: D   32 VAL cc_start: 0.9210 (t) cc_final: 0.8979 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 174
  average time/residue: 0.0892
  time to fit residues: 22.8278
Evaluate side-chains
  137 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 85 optimal weight:    3.9990
   chunk 7 optimal weight:    6.9990
   chunk 99 optimal weight:    4.9990
   chunk 15 optimal weight:    5.9990
   chunk 76 optimal weight:    5.9990
   chunk 29 optimal weight:    6.9990
   chunk 93 optimal weight:    9.9990
   chunk 2 optimal weight:    4.9990
   chunk 72 optimal weight:    9.9990
   chunk 60 optimal weight:    3.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.048218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.041351 restraints weight = 77066.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.042286 restraints weight = 50222.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 18)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.042857 restraints weight = 36976.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.043396 restraints weight = 29928.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.043761 restraints weight = 24938.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.6675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   9899  Z= 0.217
  Angle     :  0.772  11.668  13498  Z= 0.398
  Chirality :  0.044   0.187   1560
  Planarity :  0.006   0.084   1680
  Dihedral  :  5.855  29.061   1319
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 20.08
  Ramachandran Plot:
    Outliers :  0.83 %
    Allowed  :  8.52 %
    Favored  : 90.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.86 (0.24), residues: 1209
  helix:  1.00 (0.19), residues: 687
  sheet: -2.01 (0.48), residues: 113
  loop : -2.96 (0.29), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 496 
 TYR   0.023   0.002   TYR C  90 
 PHE   0.031   0.002   PHE A 302 
 TRP   0.022   0.002   TRP D  67 
 HIS   0.008   0.002   HIS C  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 ( 9894)
  covalent geometry    : angle       0.76731 (13488)
  SS BOND              : bond        0.00894 (    5)
  SS BOND              : angle       3.12922 (   10)
  hydrogen bonds       : bond        0.04475 (  564)
  hydrogen bonds       : angle       4.97720 ( 1671)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 LEU cc_start: 0.9189 (tp) cc_final: 0.8973 (tp)
REVERT: A  182 LEU cc_start: 0.9522 (tp) cc_final: 0.9064 (pp)
REVERT: A  347 MET cc_start: 0.9185 (mmp) cc_final: 0.8506 (mmp)
REVERT: A  538 LEU cc_start: 0.9399 (mt) cc_final: 0.9034 (tp)
REVERT: A  553 HIS cc_start: 0.8527 (m90) cc_final: 0.8298 (m90)
REVERT: A  554 TYR cc_start: 0.8947 (t80) cc_final: 0.8690 (t80)
REVERT: B   84 MET cc_start: 0.9332 (mtm) cc_final: 0.8980 (mmt)
REVERT: B   92 CYS cc_start: 0.8645 (t) cc_final: 0.8164 (t)
REVERT: B  184 GLU cc_start: 0.9392 (mm-30) cc_final: 0.9017 (mm-30)
REVERT: B  195 TYR cc_start: 0.9179 (m-10) cc_final: 0.8520 (m-10)
REVERT: B  221 LEU cc_start: 0.8774 (mt) cc_final: 0.7779 (mt)
REVERT: B  225 TYR cc_start: 0.8863 (m-10) cc_final: 0.8549 (m-80)
REVERT: B  386 PHE cc_start: 0.8633 (t80) cc_final: 0.8266 (t80)
REVERT: B  457 MET cc_start: 0.9676 (mmp) cc_final: 0.9449 (mmm)
REVERT: B  459 GLN cc_start: 0.9230 (tp40) cc_final: 0.8967 (tp40)
REVERT: C   35 LEU cc_start: 0.9660 (mm) cc_final: 0.9365 (mm)
REVERT: C   53 TRP cc_start: 0.8952 (t60) cc_final: 0.8554 (t60)
REVERT: C   84 GLU cc_start: 0.9346 (pp20) cc_final: 0.9073 (pp20)
REVERT: C   86 PHE cc_start: 0.9177 (m-10) cc_final: 0.8875 (m-10)
REVERT: C   98 ASP cc_start: 0.9508 (t0) cc_final: 0.9168 (m-30)
REVERT: C  109 ARG cc_start: 0.8258 (pmt-80) cc_final: 0.7902 (ptm-80)
REVERT: C  119 TYR cc_start: 0.9167 (t80) cc_final: 0.8935 (t80)
REVERT: C  132 PHE cc_start: 0.9262 (m-10) cc_final: 0.8951 (m-10)
REVERT: C  167 ILE cc_start: 0.9748 (tt) cc_final: 0.9337 (tt)
REVERT: C  171 HIS cc_start: 0.9529 (m90) cc_final: 0.8698 (m90)
REVERT: C  218 TYR cc_start: 0.9469 (m-80) cc_final: 0.8847 (m-80)
REVERT: D   32 VAL cc_start: 0.9247 (t) cc_final: 0.9022 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 0.0819
  time to fit residues: 20.4310
Evaluate side-chains
  126 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 41 optimal weight:    8.9990
   chunk 100 optimal weight:    0.9980
   chunk 45 optimal weight:    9.9990
   chunk 22 optimal weight:    8.9990
   chunk 21 optimal weight:    6.9990
   chunk 118 optimal weight:    2.9990
   chunk 104 optimal weight:   10.0000
   chunk 44 optimal weight:   10.0000
   chunk 120 optimal weight:    7.9990
   chunk 96 optimal weight:   10.0000
   chunk 83 optimal weight:   10.0000
   overall best weight:    5.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.047246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.040492 restraints weight = 78630.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.041418 restraints weight = 51213.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.042077 restraints weight = 37682.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.042551 restraints weight = 29802.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.042871 restraints weight = 24757.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.6805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   9899  Z= 0.267
  Angle     :  0.831  15.642  13498  Z= 0.429
  Chirality :  0.045   0.188   1560
  Planarity :  0.006   0.089   1680
  Dihedral  :  6.089  29.665   1319
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 23.66
  Ramachandran Plot:
    Outliers :  0.83 %
    Allowed  :  9.10 %
    Favored  : 90.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.07 (0.24), residues: 1209
  helix:  0.76 (0.19), residues: 689
  sheet: -1.98 (0.48), residues: 108
  loop : -2.95 (0.30), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 220 
 TYR   0.024   0.002   TYR A  41 
 PHE   0.034   0.002   PHE D  66 
 TRP   0.020   0.002   TRP D  36 
 HIS   0.012   0.002   HIS C 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00553 ( 9894)
  covalent geometry    : angle       0.82798 (13488)
  SS BOND              : bond        0.00957 (    5)
  SS BOND              : angle       2.86935 (   10)
  hydrogen bonds       : bond        0.04820 (  564)
  hydrogen bonds       : angle       5.20433 ( 1671)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 MET cc_start: 0.8445 (mpp) cc_final: 0.7973 (mpp)
REVERT: A   97 LEU cc_start: 0.9163 (tp) cc_final: 0.8951 (tp)
REVERT: A  182 LEU cc_start: 0.9577 (tp) cc_final: 0.9021 (pp)
REVERT: A  184 GLU cc_start: 0.9329 (tp30) cc_final: 0.9126 (tp30)
REVERT: A  347 MET cc_start: 0.9172 (mmp) cc_final: 0.8567 (mmp)
REVERT: A  378 MET cc_start: 0.8786 (mpp) cc_final: 0.8568 (mpp)
REVERT: A  430 PHE cc_start: 0.8901 (m-80) cc_final: 0.8290 (m-80)
REVERT: A  538 LEU cc_start: 0.9447 (mt) cc_final: 0.9081 (tp)
REVERT: A  553 HIS cc_start: 0.8555 (m90) cc_final: 0.8270 (m90)
REVERT: A  554 TYR cc_start: 0.8871 (t80) cc_final: 0.8618 (t80)
REVERT: A  673 LEU cc_start: 0.9647 (tt) cc_final: 0.9104 (pp)
REVERT: A  677 PHE cc_start: 0.9090 (m-10) cc_final: 0.8808 (m-80)
REVERT: B  184 GLU cc_start: 0.9365 (mm-30) cc_final: 0.8918 (mm-30)
REVERT: B  195 TYR cc_start: 0.9157 (m-10) cc_final: 0.8568 (m-10)
REVERT: B  225 TYR cc_start: 0.8810 (m-10) cc_final: 0.8511 (m-80)
REVERT: B  386 PHE cc_start: 0.8317 (t80) cc_final: 0.8014 (t80)
REVERT: B  450 ASP cc_start: 0.8605 (t70) cc_final: 0.8387 (t0)
REVERT: B  457 MET cc_start: 0.9666 (mmp) cc_final: 0.9451 (mmm)
REVERT: B  459 GLN cc_start: 0.9225 (tp40) cc_final: 0.8993 (tp40)
REVERT: C   35 LEU cc_start: 0.9693 (mm) cc_final: 0.9413 (mm)
REVERT: C   53 TRP cc_start: 0.8951 (t60) cc_final: 0.8527 (t60)
REVERT: C   84 GLU cc_start: 0.9373 (pp20) cc_final: 0.9079 (pp20)
REVERT: C   86 PHE cc_start: 0.9222 (m-10) cc_final: 0.8915 (m-10)
REVERT: C   99 GLU cc_start: 0.8393 (pt0) cc_final: 0.8124 (pp20)
REVERT: C  119 TYR cc_start: 0.9200 (t80) cc_final: 0.8942 (t80)
REVERT: C  132 PHE cc_start: 0.9203 (m-10) cc_final: 0.8920 (m-10)
REVERT: C  167 ILE cc_start: 0.9716 (tt) cc_final: 0.9304 (tt)
REVERT: C  171 HIS cc_start: 0.9403 (m90) cc_final: 0.8619 (m90)
REVERT: C  218 TYR cc_start: 0.9469 (m-80) cc_final: 0.8726 (m-80)
REVERT: D   32 VAL cc_start: 0.9270 (t) cc_final: 0.9030 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 0.0848
  time to fit residues: 19.3538
Evaluate side-chains
  123 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 66 optimal weight:    9.9990
   chunk 105 optimal weight:   10.0000
   chunk 96 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 83 optimal weight:    4.9990
   chunk 67 optimal weight:    7.9990
   chunk 14 optimal weight:    6.9990
   chunk 2 optimal weight:    7.9990
   chunk 41 optimal weight:   10.0000
   chunk 56 optimal weight:    4.9990
   chunk 70 optimal weight:    8.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.047439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.040648 restraints weight = 77661.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.041601 restraints weight = 50648.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.042288 restraints weight = 37094.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.042740 restraints weight = 29192.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.043063 restraints weight = 24213.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.6927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   9899  Z= 0.237
  Angle     :  0.800  11.741  13498  Z= 0.415
  Chirality :  0.045   0.193   1560
  Planarity :  0.006   0.090   1680
  Dihedral  :  6.035  30.218   1319
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 21.90
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  :  9.59 %
    Favored  : 89.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 1.85 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.04 (0.24), residues: 1209
  helix:  0.78 (0.19), residues: 688
  sheet: -2.00 (0.47), residues: 108
  loop : -2.90 (0.30), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 434 
 TYR   0.023   0.002   TYR C  90 
 PHE   0.031   0.002   PHE A 302 
 TRP   0.018   0.002   TRP B 247 
 HIS   0.010   0.002   HIS C  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 ( 9894)
  covalent geometry    : angle       0.79647 (13488)
  SS BOND              : bond        0.00956 (    5)
  SS BOND              : angle       2.88311 (   10)
  hydrogen bonds       : bond        0.04710 (  564)
  hydrogen bonds       : angle       5.15011 ( 1671)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1498.76 seconds
wall clock time: 26 minutes 50.57 seconds (1610.57 seconds total)