Starting phenix.real_space_refine
on Wed Apr 30 16:49:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5fn5_3240/04_2025/5fn5_3240.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5fn5_3240/04_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5fn5_3240/04_2025/5fn5_3240.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5fn5_3240/04_2025/5fn5_3240.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5fn5_3240/04_2025/5fn5_3240.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5fn5_3240/04_2025/5fn5_3240.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'TYR:plan': 1, 'GLU:plan': 5, 'ASP: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: 5.88, per 1000 atoms: 0.61
  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: 2.42
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  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: 0.87
  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: 2.84

  Time building geometry restraints manager: 2.87 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:             0.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     24.340
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.470
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.031   0.004   TRP D  36 
 HIS   0.013   0.003   HIS A  74 
 PHE   0.059   0.005   PHE A 302 
 TYR   0.042   0.004   TYR B 225 
 ARG   0.008   0.001   ARG A 657 

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

*********************** 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  : 1.074 
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: symmetry clash
REVERT: A   64 SER cc_start: 0.6710 (OUTLIER) cc_final: 0.6345 (p)
REVERT: A   95 MET cc_start: 0.9170 (mmt) cc_final: 0.8700 (mmm)
REVERT: A  129 SER cc_start: 0.7373 (OUTLIER) cc_final: 0.6535 (t)
REVERT: A  237 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8194 (tp-100)
REVERT: A  333 GLU cc_start: 0.9323 (OUTLIER) cc_final: 0.8792 (mp0)
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: 0.9433 (mt)
REVERT: A  555 ILE cc_start: 0.7981 (mt) cc_final: 0.6549 (mt)
REVERT: A  574 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8803 (mt)
REVERT: A  624 THR cc_start: 0.7194 (OUTLIER) cc_final: 0.6823 (m)
REVERT: A  644 GLU cc_start: 0.9115 (OUTLIER) cc_final: 0.8895 (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: 0.9022 (mttm)
REVERT: B  105 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8396 (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: 0.8142 (p0)
REVERT: B  195 TYR cc_start: 0.8934 (OUTLIER) cc_final: 0.8656 (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: 0.8514 (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: 0.9275 (mp10)
REVERT: C   84 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8619 (mm-30)
REVERT: C  132 PHE cc_start: 0.9522 (m-10) cc_final: 0.9304 (m-10)
REVERT: C  136 ASN cc_start: 0.9112 (m-40) cc_final: 0.8562 (p0)
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)
REVERT: D   96 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7658 (mm)
  outliers start: 146
  outliers final: 47
  residues processed: 346
  average time/residue: 0.2063
  time to fit residues: 99.7033
Evaluate side-chains
  223 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 160
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 102 optimal weight:    9.9990
   chunk 91 optimal weight:    5.9990
   chunk 50 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 94 optimal weight:    6.9990
   chunk 36 optimal weight:    3.9990
   chunk 57 optimal weight:    8.9990
   chunk 70 optimal weight:    0.4980
   chunk 109 optimal weight:    5.9990
   overall best weight:    2.2988

-------------------------------------------------------------------------------
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 = 0.3227 r_free = 0.3227 target = 0.053476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.045789 restraints weight = 68223.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.046864 restraints weight = 44552.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.047687 restraints weight = 32279.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.4183

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= 0.199
  Angle     :  0.876  11.272  13498  Z= 0.456
  Chirality :  0.048   0.197   1560
  Planarity :  0.006   0.090   1680
  Dihedral  :  7.200  35.800   1319
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 17.12
  Ramachandran Plot:
    Outliers :  1.08 %
    Allowed  :  8.35 %
    Favored  : 90.57 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  3.93 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.25), residues: 1209
  helix:  1.87 (0.20), residues: 692
  sheet: -2.88 (0.44), residues: 109
  loop : -3.92 (0.25), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 257 
 HIS   0.009   0.002   HIS A 553 
 PHE   0.038   0.003   PHE A 302 
 TYR   0.023   0.002   TYR C  69 
 ARG   0.004   0.001   ARG A 117 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05435 (  564)
  hydrogen bonds       : angle       5.32435 ( 1671)
  SS BOND              : bond        0.01157 (    5)
  SS BOND              : angle       2.92674 (   10)
  covalent geometry    : bond        0.00430 ( 9894)
  covalent geometry    : angle       0.87301 (13488)

*********************** 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
  234 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 225
  time to evaluate  : 1.017 
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: A  251 LEU cc_start: 0.9404 (mt) cc_final: 0.9053 (mt)
REVERT: A  305 GLN cc_start: 0.9464 (tp-100) cc_final: 0.9132 (tt0)
REVERT: A  349 LYS cc_start: 0.9518 (mmtt) cc_final: 0.9168 (mmtp)
REVERT: A  430 PHE cc_start: 0.8993 (m-80) cc_final: 0.8749 (m-80)
REVERT: A  457 TYR cc_start: 0.8354 (m-80) cc_final: 0.7874 (m-80)
REVERT: A  538 LEU cc_start: 0.9346 (mt) cc_final: 0.9028 (mt)
REVERT: A  553 HIS cc_start: 0.9122 (m-70) cc_final: 0.8875 (m90)
REVERT: A  655 ASP cc_start: 0.8769 (m-30) cc_final: 0.8448 (p0)
REVERT: A  657 ARG cc_start: 0.9080 (ptt-90) cc_final: 0.8656 (ptt90)
REVERT: A  670 LEU cc_start: 0.9641 (mt) cc_final: 0.9412 (mt)
REVERT: A  673 LEU cc_start: 0.9556 (tt) cc_final: 0.9236 (pp)
REVERT: B  171 LEU cc_start: 0.9802 (tt) cc_final: 0.9586 (tp)
REVERT: B  194 ASP cc_start: 0.9124 (p0) cc_final: 0.8439 (p0)
REVERT: B  225 TYR cc_start: 0.8825 (m-10) cc_final: 0.8507 (m-80)
REVERT: B  450 ASP cc_start: 0.9259 (t70) cc_final: 0.8985 (p0)
REVERT: B  457 MET cc_start: 0.9546 (mmp) cc_final: 0.9209 (ptt)
REVERT: C   86 PHE cc_start: 0.9153 (m-10) cc_final: 0.8850 (m-10)
REVERT: C   99 GLU cc_start: 0.8203 (pt0) cc_final: 0.7964 (pp20)
REVERT: C  109 ARG cc_start: 0.8235 (pmt-80) cc_final: 0.7966 (ptm-80)
REVERT: C  135 ILE cc_start: 0.9239 (tp) cc_final: 0.8973 (tp)
REVERT: C  140 ASP cc_start: 0.8052 (m-30) cc_final: 0.7003 (m-30)
REVERT: C  197 HIS cc_start: 0.9697 (t-170) cc_final: 0.9179 (t-170)
REVERT: D   28 PHE cc_start: 0.9137 (t80) cc_final: 0.8880 (t80)
REVERT: D   69 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8885 (tp)
  outliers start: 9
  outliers final: 2
  residues processed: 230
  average time/residue: 0.1927
  time to fit residues: 64.3512
Evaluate side-chains
  151 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 148
  time to evaluate  : 1.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 96 optimal weight:   10.0000
   chunk 117 optimal weight:   20.0000
   chunk 82 optimal weight:    7.9990
   chunk 110 optimal weight:   20.0000
   chunk 101 optimal weight:    1.9990
   chunk 18 optimal weight:    7.9990
   chunk 27 optimal weight:    9.9990
   chunk 21 optimal weight:    9.9990
   chunk 62 optimal weight:    0.9980
   chunk 36 optimal weight:    4.9990
   chunk 61 optimal weight:   10.0000
   overall best weight:    4.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 420 GLN
** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 606 GLN
** 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 = 0.3140 r_free = 0.3140 target = 0.049955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.042893 restraints weight = 78055.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.043720 restraints weight = 50760.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.044513 restraints weight = 37899.203|
|-----------------------------------------------------------------------------|
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.5033

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= 0.245
  Angle     :  0.817  11.057  13498  Z= 0.425
  Chirality :  0.045   0.173   1560
  Planarity :  0.006   0.097   1680
  Dihedral  :  6.675  33.737   1319
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 19.93
  Ramachandran Plot:
    Outliers :  0.91 %
    Allowed  :  9.10 %
    Favored  : 89.99 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  6.52 %
    Favored  : 93.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 1.85 %
    Twisted General : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.07 (0.24), residues: 1209
  helix:  1.10 (0.19), residues: 688
  sheet: -2.58 (0.45), residues: 110
  loop : -3.44 (0.28), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A  84 
 HIS   0.009   0.002   HIS C  58 
 PHE   0.035   0.003   PHE A 302 
 TYR   0.022   0.002   TYR B 446 
 ARG   0.010   0.001   ARG A 659 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05011 (  564)
  hydrogen bonds       : angle       5.19502 ( 1671)
  SS BOND              : bond        0.01516 (    5)
  SS BOND              : angle       2.59209 (   10)
  covalent geometry    : bond        0.00506 ( 9894)
  covalent geometry    : angle       0.81392 (13488)

*********************** 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
  185 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 182
  time to evaluate  : 1.083 
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: 0.8776 (mmt) cc_final: 0.8210 (mmt)
REVERT: A   97 LEU cc_start: 0.9450 (tp) cc_final: 0.9201 (tp)
REVERT: A  147 VAL cc_start: 0.7997 (OUTLIER) cc_final: 0.7569 (m)
REVERT: A  182 LEU cc_start: 0.9711 (tp) cc_final: 0.9237 (pp)
REVERT: A  347 MET cc_start: 0.9160 (mmp) cc_final: 0.8576 (tpp)
REVERT: A  378 MET cc_start: 0.8768 (mpp) cc_final: 0.8527 (mpp)
REVERT: A  457 TYR cc_start: 0.8314 (m-80) cc_final: 0.8085 (m-80)
REVERT: A  538 LEU cc_start: 0.9488 (mt) cc_final: 0.9123 (mt)
REVERT: A  657 ARG cc_start: 0.8939 (ptt-90) cc_final: 0.8115 (ptt90)
REVERT: A  675 VAL cc_start: 0.9220 (t) cc_final: 0.9004 (p)
REVERT: A  680 LEU cc_start: 0.9478 (tp) cc_final: 0.9272 (tt)
REVERT: B   92 CYS cc_start: 0.8837 (t) cc_final: 0.7988 (t)
REVERT: B  194 ASP cc_start: 0.9134 (p0) cc_final: 0.8572 (p0)
REVERT: B  225 TYR cc_start: 0.8906 (m-10) cc_final: 0.8568 (m-80)
REVERT: B  228 MET cc_start: 0.9536 (mpp) cc_final: 0.9328 (mmt)
REVERT: B  233 MET cc_start: 0.9043 (tpt) cc_final: 0.8782 (tpp)
REVERT: B  386 PHE cc_start: 0.8725 (t80) cc_final: 0.7711 (t80)
REVERT: B  391 VAL cc_start: 0.9535 (t) cc_final: 0.9275 (t)
REVERT: B  450 ASP cc_start: 0.9024 (t70) cc_final: 0.8819 (p0)
REVERT: B  457 MET cc_start: 0.9651 (mmp) cc_final: 0.9414 (mmm)
REVERT: C   86 PHE cc_start: 0.9213 (m-10) cc_final: 0.8906 (m-10)
REVERT: C  132 PHE cc_start: 0.9435 (m-10) cc_final: 0.9194 (m-10)
REVERT: C  140 ASP cc_start: 0.8723 (m-30) cc_final: 0.8259 (m-30)
REVERT: C  197 HIS cc_start: 0.9609 (t-170) cc_final: 0.9147 (t-170)
REVERT: C  218 TYR cc_start: 0.9420 (m-80) cc_final: 0.9109 (m-80)
REVERT: D   69 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.8956 (tp)
  outliers start: 3
  outliers final: 1
  residues processed: 184
  average time/residue: 0.1873
  time to fit residues: 50.9617
Evaluate side-chains
  134 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 131
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 31 optimal weight:    0.8980
   chunk 1 optimal weight:   20.0000
   chunk 82 optimal weight:    0.9990
   chunk 42 optimal weight:    9.9990
   chunk 106 optimal weight:    0.0020
   chunk 112 optimal weight:    5.9990
   chunk 83 optimal weight:    5.9990
   chunk 102 optimal weight:    5.9990
   chunk 48 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 55 optimal weight:   10.0000
   overall best weight:    1.9794

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3191 r_free = 0.3191 target = 0.051493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.044185 restraints weight = 74272.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.045174 restraints weight = 48771.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.045956 restraints weight = 35772.027|
|-----------------------------------------------------------------------------|
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.5594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9899  Z= 0.163
  Angle     :  0.759  11.337  13498  Z= 0.391
  Chirality :  0.044   0.203   1560
  Planarity :  0.006   0.092   1680
  Dihedral  :  6.156  32.646   1319
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 16.71
  Ramachandran Plot:
    Outliers :  0.91 %
    Allowed  :  6.78 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.55 %
    Favored  : 96.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 1.85 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.25), residues: 1209
  helix:  1.28 (0.19), residues: 695
  sheet: -2.30 (0.46), residues: 110
  loop : -3.26 (0.29), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D  67 
 HIS   0.006   0.001   HIS A  74 
 PHE   0.031   0.002   PHE A 302 
 TYR   0.018   0.002   TYR C  90 
 ARG   0.003   0.000   ARG A 117 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04602 (  564)
  hydrogen bonds       : angle       4.85469 ( 1671)
  SS BOND              : bond        0.01375 (    5)
  SS BOND              : angle       2.75220 (   10)
  covalent geometry    : bond        0.00347 ( 9894)
  covalent geometry    : angle       0.75519 (13488)

*********************** 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: 1
    poor density    : 194
  time to evaluate  : 1.003 
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   97 LEU cc_start: 0.9472 (tp) cc_final: 0.9233 (tp)
REVERT: A  182 LEU cc_start: 0.9654 (tp) cc_final: 0.9254 (pp)
REVERT: A  330 PHE cc_start: 0.8890 (m-80) cc_final: 0.8550 (m-80)
REVERT: A  347 MET cc_start: 0.9130 (mmp) cc_final: 0.8422 (tpp)
REVERT: A  378 MET cc_start: 0.8812 (mpp) cc_final: 0.8565 (mpp)
REVERT: A  538 LEU cc_start: 0.9435 (mt) cc_final: 0.9137 (mt)
REVERT: A  554 TYR cc_start: 0.8846 (t80) cc_final: 0.8590 (t80)
REVERT: A  670 LEU cc_start: 0.9774 (mt) cc_final: 0.9526 (pp)
REVERT: A  673 LEU cc_start: 0.9564 (tt) cc_final: 0.9177 (pp)
REVERT: A  684 LEU cc_start: 0.9467 (mm) cc_final: 0.9245 (mm)
REVERT: B  194 ASP cc_start: 0.8866 (p0) cc_final: 0.8453 (p0)
REVERT: B  221 LEU cc_start: 0.8734 (mt) cc_final: 0.7884 (mt)
REVERT: B  228 MET cc_start: 0.9458 (mpp) cc_final: 0.9173 (mmt)
REVERT: B  457 MET cc_start: 0.9578 (mmp) cc_final: 0.9369 (mmp)
REVERT: B  459 GLN cc_start: 0.9349 (tp40) cc_final: 0.9051 (tp40)
REVERT: C   84 GLU cc_start: 0.9363 (pp20) cc_final: 0.9032 (pp20)
REVERT: C   86 PHE cc_start: 0.9212 (m-10) cc_final: 0.8882 (m-10)
REVERT: C   99 GLU cc_start: 0.8651 (pt0) cc_final: 0.8397 (pp20)
REVERT: C  109 ARG cc_start: 0.8255 (pmt-80) cc_final: 0.7669 (ptm-80)
REVERT: C  132 PHE cc_start: 0.9517 (m-10) cc_final: 0.8837 (m-10)
REVERT: C  218 TYR cc_start: 0.9537 (m-80) cc_final: 0.9320 (m-80)
REVERT: D   47 TYR cc_start: 0.7480 (m-80) cc_final: 0.7187 (m-80)
REVERT: D   69 ILE cc_start: 0.9303 (OUTLIER) cc_final: 0.9003 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 195
  average time/residue: 0.1790
  time to fit residues: 51.5391
Evaluate side-chains
  137 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 136
  time to evaluate  : 1.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 17 optimal weight:    0.0470
   chunk 112 optimal weight:    4.9990
   chunk 87 optimal weight:    6.9990
   chunk 119 optimal weight:    7.9990
   chunk 80 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9990
   chunk 105 optimal weight:   10.0000
   chunk 2 optimal weight:    2.9990
   chunk 84 optimal weight:    7.9990
   chunk 52 optimal weight:    4.9990
   chunk 90 optimal weight:   10.0000
   overall best weight:    2.8086

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

Flipped N/Q/H residues before XYZ refinement:
** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 454 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.050885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.043628 restraints weight = 72568.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.044634 restraints weight = 46548.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.045229 restraints weight = 34093.245|
|-----------------------------------------------------------------------------|
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.5973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9899  Z= 0.178
  Angle     :  0.747  11.267  13498  Z= 0.385
  Chirality :  0.044   0.191   1560
  Planarity :  0.006   0.087   1680
  Dihedral  :  5.934  30.908   1319
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 18.06
  Ramachandran Plot:
    Outliers :  0.83 %
    Allowed  :  8.27 %
    Favored  : 90.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 1.85 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.70 (0.25), residues: 1209
  helix:  1.27 (0.19), residues: 694
  sheet: -2.36 (0.46), residues: 113
  loop : -3.10 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP C  42 
 HIS   0.006   0.001   HIS C  58 
 PHE   0.041   0.002   PHE C 205 
 TYR   0.024   0.002   TYR A 457 
 ARG   0.005   0.000   ARG A 117 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04427 (  564)
  hydrogen bonds       : angle       4.81023 ( 1671)
  SS BOND              : bond        0.00836 (    5)
  SS BOND              : angle       2.71211 (   10)
  covalent geometry    : bond        0.00386 ( 9894)
  covalent geometry    : angle       0.74345 (13488)

*********************** 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
  178 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 1.038 
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   37 GLU cc_start: 0.9267 (pt0) cc_final: 0.8721 (tm-30)
REVERT: A  182 LEU cc_start: 0.9644 (tp) cc_final: 0.9251 (pp)
REVERT: A  213 CYS cc_start: 0.5544 (t) cc_final: 0.5216 (t)
REVERT: A  231 MET cc_start: 0.9497 (ttt) cc_final: 0.9248 (ttm)
REVERT: A  260 LEU cc_start: 0.9341 (tt) cc_final: 0.9122 (tt)
REVERT: A  347 MET cc_start: 0.9185 (mmp) cc_final: 0.8827 (mmp)
REVERT: A  378 MET cc_start: 0.8768 (mpp) cc_final: 0.8551 (mpp)
REVERT: A  538 LEU cc_start: 0.9460 (mt) cc_final: 0.9088 (mt)
REVERT: A  553 HIS cc_start: 0.8854 (m90) cc_final: 0.8534 (m90)
REVERT: A  554 TYR cc_start: 0.9001 (t80) cc_final: 0.8704 (t80)
REVERT: A  670 LEU cc_start: 0.9781 (mt) cc_final: 0.9567 (pp)
REVERT: A  684 LEU cc_start: 0.9460 (mm) cc_final: 0.9232 (mm)
REVERT: B  194 ASP cc_start: 0.9091 (p0) cc_final: 0.8351 (p0)
REVERT: B  195 TYR cc_start: 0.9222 (m-80) cc_final: 0.8953 (m-80)
REVERT: B  233 MET cc_start: 0.9264 (mmp) cc_final: 0.8850 (tpp)
REVERT: B  386 PHE cc_start: 0.8529 (t80) cc_final: 0.8121 (t80)
REVERT: B  441 PHE cc_start: 0.9464 (m-80) cc_final: 0.8776 (m-80)
REVERT: B  457 MET cc_start: 0.9672 (mmp) cc_final: 0.9376 (mmp)
REVERT: B  459 GLN cc_start: 0.9233 (tp40) cc_final: 0.8925 (tp40)
REVERT: C   53 TRP cc_start: 0.8968 (t60) cc_final: 0.8666 (t60)
REVERT: C   84 GLU cc_start: 0.9382 (pp20) cc_final: 0.9062 (pp20)
REVERT: C   86 PHE cc_start: 0.9127 (m-10) cc_final: 0.8842 (m-10)
REVERT: C   99 GLU cc_start: 0.8665 (pt0) cc_final: 0.8434 (pp20)
REVERT: C  132 PHE cc_start: 0.9323 (m-10) cc_final: 0.9049 (m-10)
REVERT: C  218 TYR cc_start: 0.9543 (m-80) cc_final: 0.9306 (m-80)
REVERT: D   28 PHE cc_start: 0.9110 (t80) cc_final: 0.8825 (t80)
REVERT: D   32 VAL cc_start: 0.9330 (t) cc_final: 0.9123 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 178
  average time/residue: 0.1796
  time to fit residues: 47.5974
Evaluate side-chains
  131 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 1.040 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 106 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 61 optimal weight:    9.9990
   chunk 54 optimal weight:    0.1980
   chunk 89 optimal weight:   10.0000
   chunk 73 optimal weight:   10.0000
   chunk 32 optimal weight:    9.9990
   chunk 107 optimal weight:    5.9990
   chunk 60 optimal weight:    4.9990
   chunk 36 optimal weight:    9.9990
   chunk 71 optimal weight:    9.9990
   overall best weight:    6.0388

-------------------------------------------------------------------------------
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 379 HIS
A 449 HIS
** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 454 GLN
** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.048295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.041331 restraints weight = 77758.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.042315 restraints weight = 49648.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.043055 restraints weight = 35871.686|
|-----------------------------------------------------------------------------|
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.6171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   9899  Z= 0.287
  Angle     :  0.834  11.504  13498  Z= 0.435
  Chirality :  0.045   0.180   1560
  Planarity :  0.006   0.081   1680
  Dihedral  :  6.177  31.030   1319
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 22.10
  Ramachandran Plot:
    Outliers :  0.83 %
    Allowed  :  8.93 %
    Favored  : 90.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 1.85 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.01 (0.24), residues: 1209
  helix:  0.98 (0.19), residues: 686
  sheet: -2.48 (0.45), residues: 115
  loop : -3.07 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A  84 
 HIS   0.009   0.002   HIS A 102 
 PHE   0.030   0.002   PHE A 302 
 TYR   0.025   0.002   TYR C  90 
 ARG   0.004   0.001   ARG A 285 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04943 (  564)
  hydrogen bonds       : angle       5.18069 ( 1671)
  SS BOND              : bond        0.01377 (    5)
  SS BOND              : angle       2.71901 (   10)
  covalent geometry    : bond        0.00595 ( 9894)
  covalent geometry    : angle       0.83092 (13488)

*********************** 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
  166 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 1.105 
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   37 GLU cc_start: 0.9278 (pt0) cc_final: 0.8795 (tm-30)
REVERT: A   95 MET cc_start: 0.8379 (mpp) cc_final: 0.7528 (mpp)
REVERT: A  103 PHE cc_start: 0.9389 (t80) cc_final: 0.8923 (t80)
REVERT: A  108 MET cc_start: 0.9085 (mmp) cc_final: 0.8869 (mmp)
REVERT: A  182 LEU cc_start: 0.9663 (tp) cc_final: 0.9139 (pp)
REVERT: A  213 CYS cc_start: 0.5739 (t) cc_final: 0.5304 (t)
REVERT: A  260 LEU cc_start: 0.9300 (tt) cc_final: 0.9063 (tt)
REVERT: A  347 MET cc_start: 0.9234 (mmp) cc_final: 0.8926 (mmp)
REVERT: A  378 MET cc_start: 0.8821 (mpp) cc_final: 0.8499 (mpp)
REVERT: A  538 LEU cc_start: 0.9406 (mt) cc_final: 0.9024 (tp)
REVERT: A  554 TYR cc_start: 0.8927 (t80) cc_final: 0.8643 (t80)
REVERT: A  657 ARG cc_start: 0.8634 (ptt-90) cc_final: 0.8407 (ptt-90)
REVERT: A  677 PHE cc_start: 0.9139 (m-10) cc_final: 0.8693 (m-80)
REVERT: A  684 LEU cc_start: 0.9444 (mm) cc_final: 0.9208 (mm)
REVERT: B  195 TYR cc_start: 0.9263 (m-80) cc_final: 0.9030 (m-80)
REVERT: B  225 TYR cc_start: 0.9015 (m-80) cc_final: 0.8511 (m-80)
REVERT: B  227 ILE cc_start: 0.9388 (pt) cc_final: 0.9177 (pt)
REVERT: B  386 PHE cc_start: 0.8611 (t80) cc_final: 0.8342 (t80)
REVERT: B  457 MET cc_start: 0.9702 (mmp) cc_final: 0.9369 (mmm)
REVERT: B  459 GLN cc_start: 0.9268 (tp40) cc_final: 0.8975 (tp40)
REVERT: C   53 TRP cc_start: 0.9017 (t60) cc_final: 0.8593 (t60)
REVERT: C   84 GLU cc_start: 0.9421 (pp20) cc_final: 0.9098 (pp20)
REVERT: C   86 PHE cc_start: 0.9170 (m-10) cc_final: 0.8867 (m-10)
REVERT: C   99 GLU cc_start: 0.8665 (pt0) cc_final: 0.8424 (pp20)
REVERT: C  119 TYR cc_start: 0.9252 (t80) cc_final: 0.8967 (t80)
REVERT: C  132 PHE cc_start: 0.9248 (m-10) cc_final: 0.8969 (m-10)
REVERT: C  218 TYR cc_start: 0.9510 (m-80) cc_final: 0.9182 (m-80)
REVERT: D   28 PHE cc_start: 0.9022 (t80) cc_final: 0.8805 (t80)
REVERT: D   32 VAL cc_start: 0.9367 (t) cc_final: 0.9086 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.1844
  time to fit residues: 45.3160
Evaluate side-chains
  132 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 113 optimal weight:   20.0000
   chunk 80 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 55 optimal weight:    8.9990
   chunk 56 optimal weight:    0.7980
   chunk 93 optimal weight:    7.9990
   chunk 49 optimal weight:    9.9990
   chunk 14 optimal weight:    8.9990
   chunk 65 optimal weight:    5.9990
   chunk 58 optimal weight:    8.9990
   chunk 89 optimal weight:    5.9990
   overall best weight:    5.5588

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.047604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.040747 restraints weight = 76842.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.041679 restraints weight = 48893.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.042431 restraints weight = 35398.475|
|-----------------------------------------------------------------------------|
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.6389

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= 0.263
  Angle     :  0.810  11.523  13498  Z= 0.421
  Chirality :  0.045   0.180   1560
  Planarity :  0.006   0.083   1680
  Dihedral  :  6.175  30.094   1319
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 23.19
  Ramachandran Plot:
    Outliers :  0.83 %
    Allowed  :  9.26 %
    Favored  : 89.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 1.85 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.18 (0.24), residues: 1209
  helix:  0.79 (0.19), residues: 696
  sheet: -2.38 (0.46), residues: 115
  loop : -3.17 (0.29), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP D  67 
 HIS   0.007   0.002   HIS A 553 
 PHE   0.029   0.003   PHE A 302 
 TYR   0.022   0.002   TYR B 106 
 ARG   0.005   0.001   ARG A 434 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04742 (  564)
  hydrogen bonds       : angle       5.14841 ( 1671)
  SS BOND              : bond        0.01030 (    5)
  SS BOND              : angle       2.83006 (   10)
  covalent geometry    : bond        0.00545 ( 9894)
  covalent geometry    : angle       0.80666 (13488)

*********************** 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
  160 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 1.009 
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   37 GLU cc_start: 0.9279 (pt0) cc_final: 0.8806 (tm-30)
REVERT: A   95 MET cc_start: 0.8468 (mpp) cc_final: 0.8040 (mpp)
REVERT: A  182 LEU cc_start: 0.9566 (tp) cc_final: 0.9028 (pp)
REVERT: A  343 MET cc_start: 0.9450 (tpt) cc_final: 0.9173 (tpp)
REVERT: A  347 MET cc_start: 0.9252 (mmp) cc_final: 0.8958 (mmp)
REVERT: A  378 MET cc_start: 0.8856 (mpp) cc_final: 0.8508 (mpp)
REVERT: A  430 PHE cc_start: 0.9052 (m-80) cc_final: 0.8696 (m-80)
REVERT: A  538 LEU cc_start: 0.9461 (mt) cc_final: 0.9058 (tp)
REVERT: A  553 HIS cc_start: 0.8742 (m-70) cc_final: 0.8515 (m90)
REVERT: A  657 ARG cc_start: 0.8724 (ptt-90) cc_final: 0.8416 (ptt-90)
REVERT: B  195 TYR cc_start: 0.9283 (m-80) cc_final: 0.9024 (m-80)
REVERT: B  210 MET cc_start: 0.8980 (mmp) cc_final: 0.8703 (mmm)
REVERT: B  386 PHE cc_start: 0.8694 (t80) cc_final: 0.8400 (t80)
REVERT: B  457 MET cc_start: 0.9644 (mmp) cc_final: 0.9406 (mmp)
REVERT: B  459 GLN cc_start: 0.9297 (tp40) cc_final: 0.8984 (tp40)
REVERT: C   53 TRP cc_start: 0.9030 (t60) cc_final: 0.8535 (t60)
REVERT: C   84 GLU cc_start: 0.9426 (pp20) cc_final: 0.9101 (pp20)
REVERT: C   86 PHE cc_start: 0.9214 (m-10) cc_final: 0.8912 (m-10)
REVERT: C   99 GLU cc_start: 0.8659 (pt0) cc_final: 0.8402 (pp20)
REVERT: C  119 TYR cc_start: 0.9277 (t80) cc_final: 0.8914 (t80)
REVERT: C  132 PHE cc_start: 0.9341 (m-10) cc_final: 0.9068 (m-10)
REVERT: C  167 ILE cc_start: 0.9762 (tt) cc_final: 0.9363 (tt)
REVERT: C  171 HIS cc_start: 0.9603 (m90) cc_final: 0.8860 (m-70)
REVERT: C  218 TYR cc_start: 0.9518 (m-80) cc_final: 0.9013 (m-80)
REVERT: D   28 PHE cc_start: 0.9021 (t80) cc_final: 0.8577 (t80)
REVERT: D   32 VAL cc_start: 0.9364 (t) cc_final: 0.9059 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 0.1833
  time to fit residues: 43.2048
Evaluate side-chains
  124 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 85 optimal weight:    7.9990
   chunk 52 optimal weight:    4.9990
   chunk 46 optimal weight:    5.9990
   chunk 114 optimal weight:    8.9990
   chunk 16 optimal weight:    5.9990
   chunk 110 optimal weight:   20.0000
   chunk 70 optimal weight:    0.0770
   chunk 116 optimal weight:   10.0000
   chunk 66 optimal weight:    8.9990
   chunk 5 optimal weight:    8.9990
   chunk 18 optimal weight:   10.0000
   overall best weight:    5.0146

-------------------------------------------------------------------------------
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**
B 405 ASN
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.047864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.040898 restraints weight = 78554.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.041907 restraints weight = 49664.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.042645 restraints weight = 35779.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.6622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   9899  Z= 0.248
  Angle     :  0.815  11.653  13498  Z= 0.424
  Chirality :  0.045   0.238   1560
  Planarity :  0.006   0.082   1680
  Dihedral  :  6.172  30.478   1319
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 23.14
  Ramachandran Plot:
    Outliers :  0.83 %
    Allowed  :  8.85 %
    Favored  : 90.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 1.85 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.24), residues: 1209
  helix:  0.65 (0.19), residues: 693
  sheet: -2.43 (0.45), residues: 115
  loop : -3.05 (0.30), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP B 404 
 HIS   0.008   0.002   HIS C  58 
 PHE   0.030   0.002   PHE C 173 
 TYR   0.037   0.002   TYR A 554 
 ARG   0.004   0.001   ARG A 434 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04834 (  564)
  hydrogen bonds       : angle       5.19065 ( 1671)
  SS BOND              : bond        0.00911 (    5)
  SS BOND              : angle       3.73871 (   10)
  covalent geometry    : bond        0.00523 ( 9894)
  covalent geometry    : angle       0.80912 (13488)

*********************** 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
  158 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 1.188 
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: 0.8167 (mpp)
REVERT: A  182 LEU cc_start: 0.9551 (tp) cc_final: 0.8981 (pp)
REVERT: A  213 CYS cc_start: 0.5362 (t) cc_final: 0.4756 (t)
REVERT: A  343 MET cc_start: 0.9449 (tpt) cc_final: 0.9228 (tpp)
REVERT: A  347 MET cc_start: 0.9253 (mmp) cc_final: 0.8672 (mmp)
REVERT: A  378 MET cc_start: 0.8899 (mpp) cc_final: 0.8509 (mpp)
REVERT: A  430 PHE cc_start: 0.9074 (m-80) cc_final: 0.8731 (m-80)
REVERT: A  538 LEU cc_start: 0.9404 (mt) cc_final: 0.9036 (tp)
REVERT: A  554 TYR cc_start: 0.8822 (t80) cc_final: 0.8548 (t80)
REVERT: A  650 GLU cc_start: 0.9143 (pt0) cc_final: 0.8661 (pm20)
REVERT: A  657 ARG cc_start: 0.8702 (ptt-90) cc_final: 0.8459 (ptt-90)
REVERT: A  677 PHE cc_start: 0.9273 (m-80) cc_final: 0.8741 (m-80)
REVERT: B   86 PHE cc_start: 0.9556 (t80) cc_final: 0.9328 (t80)
REVERT: B  195 TYR cc_start: 0.9309 (m-80) cc_final: 0.9026 (m-80)
REVERT: B  210 MET cc_start: 0.9034 (mmp) cc_final: 0.8761 (mmm)
REVERT: B  386 PHE cc_start: 0.8702 (t80) cc_final: 0.8326 (t80)
REVERT: B  457 MET cc_start: 0.9688 (mmp) cc_final: 0.9453 (mmm)
REVERT: B  459 GLN cc_start: 0.9278 (tp40) cc_final: 0.8948 (tp40)
REVERT: C   53 TRP cc_start: 0.8959 (t60) cc_final: 0.8536 (t60)
REVERT: C   84 GLU cc_start: 0.9431 (pp20) cc_final: 0.9119 (pp20)
REVERT: C   86 PHE cc_start: 0.9150 (m-10) cc_final: 0.8859 (m-10)
REVERT: C   99 GLU cc_start: 0.8665 (pt0) cc_final: 0.8407 (pp20)
REVERT: C  119 TYR cc_start: 0.9245 (t80) cc_final: 0.8884 (t80)
REVERT: C  132 PHE cc_start: 0.9202 (m-10) cc_final: 0.8857 (m-10)
REVERT: C  140 ASP cc_start: 0.8638 (m-30) cc_final: 0.8399 (m-30)
REVERT: C  167 ILE cc_start: 0.9757 (tt) cc_final: 0.9346 (tt)
REVERT: C  171 HIS cc_start: 0.9594 (m90) cc_final: 0.8813 (m-70)
REVERT: C  218 TYR cc_start: 0.9539 (m-80) cc_final: 0.8971 (m-80)
REVERT: D   28 PHE cc_start: 0.9076 (t80) cc_final: 0.8702 (t80)
REVERT: D   32 VAL cc_start: 0.9400 (t) cc_final: 0.9097 (t)
REVERT: D   68 VAL cc_start: 0.9196 (t) cc_final: 0.8993 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 158
  average time/residue: 0.2043
  time to fit residues: 47.8824
Evaluate side-chains
  125 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 1.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 114 optimal weight:    7.9990
   chunk 73 optimal weight:    6.9990
   chunk 21 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 56 optimal weight:    9.9990
   chunk 112 optimal weight:    8.9990
   chunk 85 optimal weight:    7.9990
   chunk 108 optimal weight:    2.9990
   chunk 14 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   overall best weight:    4.9990

-------------------------------------------------------------------------------
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 = 0.3118 r_free = 0.3118 target = 0.047704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.040650 restraints weight = 77597.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.041663 restraints weight = 49177.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.042367 restraints weight = 35521.317|
|-----------------------------------------------------------------------------|
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.6791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   9899  Z= 0.247
  Angle     :  0.819  11.631  13498  Z= 0.424
  Chirality :  0.045   0.191   1560
  Planarity :  0.006   0.082   1680
  Dihedral  :  6.171  30.794   1319
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 22.52
  Ramachandran Plot:
    Outliers :  0.83 %
    Allowed  :  9.26 %
    Favored  : 89.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.24), residues: 1209
  helix:  0.62 (0.19), residues: 695
  sheet: -2.40 (0.45), residues: 113
  loop : -3.01 (0.30), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP D  67 
 HIS   0.012   0.002   HIS C 197 
 PHE   0.028   0.002   PHE D  66 
 TYR   0.031   0.002   TYR A 554 
 ARG   0.004   0.001   ARG A 434 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04809 (  564)
  hydrogen bonds       : angle       5.18544 ( 1671)
  SS BOND              : bond        0.00987 (    5)
  SS BOND              : angle       3.22593 (   10)
  covalent geometry    : bond        0.00518 ( 9894)
  covalent geometry    : angle       0.81460 (13488)

*********************** 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
  156 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 1.031 
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: 0.9554 (tp) cc_final: 0.8997 (pp)
REVERT: A  347 MET cc_start: 0.9241 (mmp) cc_final: 0.8630 (mmp)
REVERT: A  378 MET cc_start: 0.8867 (mpp) cc_final: 0.8502 (mpp)
REVERT: A  430 PHE cc_start: 0.9086 (m-80) cc_final: 0.8756 (m-80)
REVERT: A  538 LEU cc_start: 0.9399 (mt) cc_final: 0.9016 (tp)
REVERT: B   86 PHE cc_start: 0.9544 (t80) cc_final: 0.9245 (t80)
REVERT: B  195 TYR cc_start: 0.9304 (m-80) cc_final: 0.9057 (m-80)
REVERT: B  227 ILE cc_start: 0.9387 (pt) cc_final: 0.9164 (pt)
REVERT: B  228 MET cc_start: 0.9513 (mpp) cc_final: 0.9296 (mmt)
REVERT: B  386 PHE cc_start: 0.8645 (t80) cc_final: 0.8409 (t80)
REVERT: B  457 MET cc_start: 0.9654 (mmp) cc_final: 0.9452 (mmm)
REVERT: B  459 GLN cc_start: 0.9271 (tp40) cc_final: 0.8982 (tp40)
REVERT: C   11 PHE cc_start: 0.9213 (m-80) cc_final: 0.8831 (m-80)
REVERT: C   53 TRP cc_start: 0.9013 (t60) cc_final: 0.8528 (t60)
REVERT: C   84 GLU cc_start: 0.9405 (pp20) cc_final: 0.9101 (pp20)
REVERT: C   86 PHE cc_start: 0.9246 (m-10) cc_final: 0.8919 (m-10)
REVERT: C   99 GLU cc_start: 0.8656 (pt0) cc_final: 0.8371 (pp20)
REVERT: C  119 TYR cc_start: 0.9268 (t80) cc_final: 0.8903 (t80)
REVERT: C  132 PHE cc_start: 0.9147 (m-10) cc_final: 0.8881 (m-10)
REVERT: C  140 ASP cc_start: 0.8578 (m-30) cc_final: 0.8346 (m-30)
REVERT: C  167 ILE cc_start: 0.9761 (tt) cc_final: 0.9371 (tt)
REVERT: C  171 HIS cc_start: 0.9546 (m90) cc_final: 0.8788 (m90)
REVERT: C  218 TYR cc_start: 0.9567 (m-80) cc_final: 0.8957 (m-80)
REVERT: D   28 PHE cc_start: 0.9089 (t80) cc_final: 0.8749 (t80)
REVERT: D   32 VAL cc_start: 0.9377 (t) cc_final: 0.9071 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 156
  average time/residue: 0.1841
  time to fit residues: 42.6630
Evaluate side-chains
  122 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 1.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 95 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 39 optimal weight:    3.9990
   chunk 5 optimal weight:    8.9990
   chunk 38 optimal weight:    5.9990
   chunk 101 optimal weight:    0.9990
   chunk 109 optimal weight:    0.9980
   chunk 59 optimal weight:    5.9990
   chunk 112 optimal weight:   30.0000
   chunk 37 optimal weight:    4.9990
   overall best weight:    1.7586

-------------------------------------------------------------------------------
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**
** 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 = 0.3189 r_free = 0.3189 target = 0.050065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.042844 restraints weight = 73818.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.043883 restraints weight = 46905.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.044624 restraints weight = 33685.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.7003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9899  Z= 0.150
  Angle     :  0.766  11.642  13498  Z= 0.388
  Chirality :  0.045   0.233   1560
  Planarity :  0.006   0.081   1680
  Dihedral  :  5.713  28.930   1319
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 15.67
  Ramachandran Plot:
    Outliers :  0.74 %
    Allowed  :  7.61 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.25), residues: 1209
  helix:  0.91 (0.19), residues: 694
  sheet: -1.93 (0.48), residues: 106
  loop : -2.87 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP D  67 
 HIS   0.009   0.001   HIS C 197 
 PHE   0.039   0.002   PHE D  66 
 TYR   0.020   0.002   TYR A 565 
 ARG   0.004   0.000   ARG D  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04514 (  564)
  hydrogen bonds       : angle       4.90192 ( 1671)
  SS BOND              : bond        0.00641 (    5)
  SS BOND              : angle       3.09252 (   10)
  covalent geometry    : bond        0.00328 ( 9894)
  covalent geometry    : angle       0.76197 (13488)

********************** 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
  168 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.993 
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: 0.9533 (tp) cc_final: 0.8920 (pp)
REVERT: A  231 MET cc_start: 0.9568 (ttt) cc_final: 0.9324 (ttm)
REVERT: A  347 MET cc_start: 0.9232 (mmp) cc_final: 0.8514 (mmp)
REVERT: A  378 MET cc_start: 0.8826 (mpp) cc_final: 0.8612 (mpp)
REVERT: A  430 PHE cc_start: 0.9048 (m-80) cc_final: 0.8732 (m-80)
REVERT: A  538 LEU cc_start: 0.9409 (mt) cc_final: 0.8963 (tp)
REVERT: A  677 PHE cc_start: 0.8949 (m-10) cc_final: 0.8603 (m-80)
REVERT: B   86 PHE cc_start: 0.9497 (t80) cc_final: 0.9235 (t80)
REVERT: B  103 VAL cc_start: 0.9344 (t) cc_final: 0.8772 (t)
REVERT: B  181 TYR cc_start: 0.9399 (t80) cc_final: 0.9054 (t80)
REVERT: B  195 TYR cc_start: 0.9317 (m-80) cc_final: 0.9037 (m-80)
REVERT: B  221 LEU cc_start: 0.8873 (mt) cc_final: 0.8173 (mt)
REVERT: B  225 TYR cc_start: 0.8921 (m-80) cc_final: 0.8660 (m-80)
REVERT: B  227 ILE cc_start: 0.9371 (pt) cc_final: 0.9162 (pt)
REVERT: B  386 PHE cc_start: 0.8575 (t80) cc_final: 0.8166 (t80)
REVERT: B  459 GLN cc_start: 0.9287 (tp40) cc_final: 0.8966 (tp40)
REVERT: C   11 PHE cc_start: 0.9144 (m-80) cc_final: 0.8855 (m-80)
REVERT: C   53 TRP cc_start: 0.9119 (t60) cc_final: 0.8599 (t60)
REVERT: C   84 GLU cc_start: 0.9366 (pp20) cc_final: 0.9105 (pp20)
REVERT: C   86 PHE cc_start: 0.9180 (m-10) cc_final: 0.8909 (m-10)
REVERT: C   99 GLU cc_start: 0.8583 (pt0) cc_final: 0.8349 (pp20)
REVERT: C  109 ARG cc_start: 0.8305 (pmt-80) cc_final: 0.7867 (ptm-80)
REVERT: C  119 TYR cc_start: 0.9222 (t80) cc_final: 0.8918 (t80)
REVERT: C  167 ILE cc_start: 0.9741 (tt) cc_final: 0.9383 (tt)
REVERT: C  171 HIS cc_start: 0.9560 (m90) cc_final: 0.8741 (m90)
REVERT: C  218 TYR cc_start: 0.9580 (m-80) cc_final: 0.9024 (m-80)
REVERT: D   32 VAL cc_start: 0.9375 (t) cc_final: 0.9152 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.1781
  time to fit residues: 44.0147
Evaluate side-chains
  129 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 71 optimal weight:   10.0000
   chunk 31 optimal weight:    8.9990
   chunk 13 optimal weight:    9.9990
   chunk 103 optimal weight:    7.9990
   chunk 54 optimal weight:    0.9990
   chunk 120 optimal weight:   10.0000
   chunk 50 optimal weight:   10.0000
   chunk 37 optimal weight:    7.9990
   chunk 109 optimal weight:    8.9990
   chunk 118 optimal weight:    3.9990
   chunk 105 optimal weight:    9.9990
   overall best weight:    5.9990

-------------------------------------------------------------------------------
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 = 0.3116 r_free = 0.3116 target = 0.047503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.040806 restraints weight = 79056.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.041771 restraints weight = 50430.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.042468 restraints weight = 36364.159|
|-----------------------------------------------------------------------------|
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.7063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   9899  Z= 0.280
  Angle     :  0.843  11.682  13498  Z= 0.436
  Chirality :  0.046   0.331   1560
  Planarity :  0.006   0.082   1680
  Dihedral  :  6.050  28.821   1319
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 23.45
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  :  9.76 %
    Favored  : 89.58 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.24), residues: 1209
  helix:  0.59 (0.19), residues: 695
  sheet: -2.23 (0.46), residues: 108
  loop : -2.88 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP B 244 
 HIS   0.008   0.002   HIS C  58 
 PHE   0.034   0.002   PHE C 132 
 TYR   0.025   0.002   TYR C  90 
 ARG   0.004   0.001   ARG A 657 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04779 (  564)
  hydrogen bonds       : angle       5.16664 ( 1671)
  SS BOND              : bond        0.00939 (    5)
  SS BOND              : angle       2.85743 (   10)
  covalent geometry    : bond        0.00581 ( 9894)
  covalent geometry    : angle       0.83946 (13488)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2748.63 seconds
wall clock time: 48 minutes 55.33 seconds (2935.33 seconds total)