Starting phenix.real_space_refine
on Mon Jul 28 12:05:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5fn3_3238/07_2025/5fn3_3238.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5fn3_3238/07_2025/5fn3_3238.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5fn3_3238/07_2025/5fn3_3238.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5fn3_3238/07_2025/5fn3_3238.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5fn3_3238/07_2025/5fn3_3238.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5fn3_3238/07_2025/5fn3_3238.cif"
  }
  resolution = 4.1
  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=   0.006
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      39      5.16       5
     C    6738      2.51       5
     N    1679      2.21       5
     O    1835      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10291
  Number of models: 1
  Model: ""
    Number of chains: 5
    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: 2234
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2234
          Classifications: {'peptide': 286}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'CIS': 7, 'PTRANS': 8, 'TRANS': 270}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 27
    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: {'PTRANS': 7, 'TRANS': 235}
          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: 847
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 847
          Classifications: {'peptide': 100}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 94}
          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
    Chain: "G"
      Number of atoms: 120
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 120
          Classifications: {'peptide': 24}
          Link IDs: {'TRANS': 23}
  Time building chain proxies: 6.25, per 1000 atoms: 0.61
  Number of scatterers: 10291
  At special positions: 0
  Unit cell: (92.4, 144.2, 110.6, 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      39     16.00
     O    1835      8.00
     N    1679      7.00
     C    6738      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=2.01
    Simple disulfide: pdb=" SG  CYS A 140 " - pdb=" SG  CYS A 159 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 195 " - pdb=" SG  CYS A 213 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 230 " - pdb=" SG  CYS A 248 " distance=2.02
    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: 2.90
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2608 Ramachandran restraints generated.
    1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2482

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 5 sheets defined
      60.4% alpha, 5.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.94
  Creating SS restraints...
    Processing helix  chain 'A' and resid 34 through 41
      removed outlier: 4.230A  pdb=" N   ARG A  38 " --> pdb=" O   ASN A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 87
      removed outlier: 3.691A  pdb=" N   LEU A  82 " --> pdb=" O   LYS A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 103
      No H-bonds generated for 'chain 'A' and resid 101 through 103'
    Processing helix  chain 'A' and resid 104 through 114
    Processing helix  chain 'A' and resid 142 through 146
    Processing helix  chain 'A' and resid 185 through 200
      removed outlier: 4.181A  pdb=" N   THR A 189 " --> pdb=" O   ASP A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 206
    Processing helix  chain 'A' and resid 226 through 240
    Processing helix  chain 'A' and resid 298 through 315
    Processing helix  chain 'A' and resid 339 through 350
    Processing helix  chain 'A' and resid 381 through 387
      removed outlier: 3.514A  pdb=" N   ASN A 387 " --> pdb=" O   VAL A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 407
      removed outlier: 3.586A  pdb=" N   GLY A 407 " --> pdb=" O   LYS A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 431
      removed outlier: 3.747A  pdb=" N   PHE A 430 " --> pdb=" O   SER A 426 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 464
    Processing helix  chain 'A' and resid 474 through 479
      removed outlier: 3.677A  pdb=" N   ASN A 478 " --> pdb=" O   GLU A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 502
    Processing helix  chain 'A' and resid 514 through 527
    Processing helix  chain 'A' and resid 531 through 537
    Processing helix  chain 'A' and resid 539 through 546
      removed outlier: 3.941A  pdb=" N   SER A 544 " --> pdb=" O   ASP A 541 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LEU A 546 " --> pdb=" O   ARG A 543 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 561 through 576
      removed outlier: 3.627A  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 693
    Processing helix  chain 'B' and resid 79 through 103
      Proline residue:  B  88  - end of helix
    Processing helix  chain 'B' and resid 126 through 156
      removed outlier: 3.909A  pdb=" N   THR B 147 " --> pdb=" O   ILE B 143 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ILE B 148 " --> pdb=" O   VAL B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 190
      removed outlier: 3.779A  pdb=" N   LEU B 173 " --> pdb=" O   SER B 169 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   SER B 178 " --> pdb=" O   LEU B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 195 through 215
    Processing helix  chain 'B' and resid 218 through 241
    Processing helix  chain 'B' and resid 242 through 262
    Processing helix  chain 'B' and resid 382 through 399
      removed outlier: 3.611A  pdb=" N   VAL B 393 " --> pdb=" O   TYR B 389 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 403 through 429
    Processing helix  chain 'B' and resid 434 through 452
      removed outlier: 3.515A  pdb=" N   SER B 438 " --> pdb=" O   ALA B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 464
      removed outlier: 4.235A  pdb=" N   PHE B 456 " --> pdb=" O   LEU B 452 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2 through 24
      Proline residue:  C  16  - end of helix
    Processing helix  chain 'C' and resid 28 through 61
    Processing helix  chain 'C' and resid 64 through 106
      removed outlier: 3.676A  pdb=" N   GLY C 100 " --> pdb=" O   LYS C  96 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   SER C 103 " --> pdb=" O   GLU C  99 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   LEU C 104 " --> pdb=" O   GLY C 100 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   SER C 105 " --> pdb=" O   LEU C 101 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   GLU C 106 " --> pdb=" O   ALA C 102 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 113 through 141
      removed outlier: 5.093A  pdb=" N   ASN C 136 " --> pdb=" O   PHE C 132 " (cutoff:3.500A)
      removed outlier: 4.980A  pdb=" N   ILE C 137 " --> pdb=" O   SER C 133 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 155 through 185
      removed outlier: 3.624A  pdb=" N   THR C 159 " --> pdb=" O   TYR C 155 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ASP C 180 " --> pdb=" O   VAL C 176 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 186 through 206
      removed outlier: 3.903A  pdb=" N   LEU C 190 " --> pdb=" O   ARG C 186 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 213 through 233
    Processing helix  chain 'C' and resid 235 through 243
      removed outlier: 3.713A  pdb=" N   ILE C 239 " --> pdb=" O   SER C 235 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   LEU C 243 " --> pdb=" O   ILE C 239 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 7 through 23
      removed outlier: 3.598A  pdb=" N   LYS D  11 " --> pdb=" O   SER D   7 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   PHE D  23 " --> pdb=" O   TYR D  19 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 26 through 37
    Processing helix  chain 'D' and resid 38 through 44
      removed outlier: 4.843A  pdb=" N   VAL D  44 " --> pdb=" O   GLU D  40 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 49 through 82
    Processing helix  chain 'D' and resid 85 through 92
    Processing helix  chain 'G' and resid 5 through 13
    Processing helix  chain 'G' and resid 16 through 24
    Processing sheet with id=AA, first strand: chain 'A' and resid 42 through 43
      removed outlier: 6.490A  pdb=" N   CYS A 213 " --> pdb=" O   ILE A  73 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ASP A  69 " --> pdb=" O   LEU A 217 " (cutoff:3.500A)
    Processing sheet with id=AB, first strand: chain 'A' and resid 53 through 54
    Processing sheet with id=AC, first strand: chain 'A' and resid 412 through 414
      removed outlier: 3.745A  pdb=" N   SER A 361 " --> pdb=" O   VAL A 275 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LEU A 365 " --> pdb=" O   ALA A 279 " (cutoff:3.500A)
    Processing sheet with id=AD, first strand: chain 'A' and resid 602 through 605
    Processing sheet with id=BA, first strand: chain 'B' and resid 193 through 194
      removed outlier: 6.842A  pdb=" N   VAL B 193 " --> pdb=" O   PHE D  94 " (cutoff:3.500A)

    627 hydrogen bonds defined for protein.
    1839 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: 3.03

  Time building geometry restraints manager: 3.39 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1684
        1.32 -     1.45: 3051
        1.45 -     1.58: 5751
        1.58 -     1.71: 10
        1.71 -     1.84: 59
  Bond restraints: 10555
  Sorted by residual:
  bond pdb=" CA  THR B 122 "
       pdb=" C   THR B 122 "
    ideal  model  delta    sigma   weight residual
    1.523  1.603 -0.080 1.34e-02 5.57e+03 3.53e+01
  bond pdb=" CA  LEU B 262 "
       pdb=" C   LEU B 262 "
    ideal  model  delta    sigma   weight residual
    1.523  1.591 -0.067 1.34e-02 5.57e+03 2.53e+01
  bond pdb=" C   ILE C 127 "
       pdb=" O   ILE C 127 "
    ideal  model  delta    sigma   weight residual
    1.237  1.290 -0.053 1.13e-02 7.83e+03 2.20e+01
  bond pdb=" CA  HIS B 214 "
       pdb=" C   HIS B 214 "
    ideal  model  delta    sigma   weight residual
    1.522  1.564 -0.042 9.30e-03 1.16e+04 2.07e+01
  bond pdb=" N   LYS B 429 "
       pdb=" CA  LYS B 429 "
    ideal  model  delta    sigma   weight residual
    1.457  1.516 -0.058 1.29e-02 6.01e+03 2.04e+01
  ... (remaining 10550 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.18: 13436
        3.18 -     6.36: 867
        6.36 -     9.54: 80
        9.54 -    12.71: 12
       12.71 -    15.89: 4
  Bond angle restraints: 14399
  Sorted by residual:
  angle pdb=" C   ASN A  91 "
        pdb=" N   PRO A  92 "
        pdb=" CA  PRO A  92 "
      ideal   model   delta    sigma   weight residual
     120.38  130.82  -10.44 1.03e+00 9.43e-01 1.03e+02
  angle pdb=" N   PRO A  92 "
        pdb=" CA  PRO A  92 "
        pdb=" C   PRO A  92 "
      ideal   model   delta    sigma   weight residual
     110.70  121.52  -10.82 1.22e+00 6.72e-01 7.87e+01
  angle pdb=" C   THR B 256 "
        pdb=" CA  THR B 256 "
        pdb=" CB  THR B 256 "
      ideal   model   delta    sigma   weight residual
     110.88   97.85   13.03 1.57e+00 4.06e-01 6.89e+01
  angle pdb=" CA  VAL B  87 "
        pdb=" C   VAL B  87 "
        pdb=" N   PRO B  88 "
      ideal   model   delta    sigma   weight residual
     120.83  115.96    4.87 6.10e-01 2.69e+00 6.38e+01
  angle pdb=" CA  PRO B 117 "
        pdb=" N   PRO B 117 "
        pdb=" CD  PRO B 117 "
      ideal   model   delta    sigma   weight residual
     112.00  101.66   10.34 1.40e+00 5.10e-01 5.45e+01
  ... (remaining 14394 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.44: 5493
       23.44 -    46.88: 557
       46.88 -    70.32: 93
       70.32 -    93.77: 17
       93.77 -   117.21: 1
  Dihedral angle restraints: 6161
    sinusoidal: 2316
      harmonic: 3845
  Sorted by residual:
  dihedral pdb=" CA  GLY B 111 "
           pdb=" C   GLY B 111 "
           pdb=" N   GLN B 112 "
           pdb=" CA  GLN B 112 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -62.79 -117.21     0      5.00e+00 4.00e-02 5.49e+02
  dihedral pdb=" CA  PRO B 117 "
           pdb=" C   PRO B 117 "
           pdb=" N   PHE B 118 "
           pdb=" CA  PHE B 118 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   87.92   92.08     0      5.00e+00 4.00e-02 3.39e+02
  dihedral pdb=" CA  ALA G  17 "
           pdb=" C   ALA G  17 "
           pdb=" N   ALA G  18 "
           pdb=" CA  ALA G  18 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   94.37   85.63     0      5.00e+00 4.00e-02 2.93e+02
  ... (remaining 6158 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.120: 1373
       0.120 -    0.241: 250
       0.241 -    0.361: 42
       0.361 -    0.482: 8
       0.482 -    0.602: 5
  Chirality restraints: 1678
  Sorted by residual:
  chirality pdb=" CA  PRO B 117 "
            pdb=" N   PRO B 117 "
            pdb=" C   PRO B 117 "
            pdb=" CB  PRO B 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.12    0.60 2.00e-01 2.50e+01 9.07e+00
  chirality pdb=" CA  THR B 122 "
            pdb=" N   THR B 122 "
            pdb=" C   THR B 122 "
            pdb=" CB  THR B 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    1.94    0.59 2.00e-01 2.50e+01 8.56e+00
  chirality pdb=" CA  PHE A 525 "
            pdb=" N   PHE A 525 "
            pdb=" C   PHE A 525 "
            pdb=" CB  PHE A 525 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.94    0.57 2.00e-01 2.50e+01 8.20e+00
  ... (remaining 1675 not shown)

  Planarity restraints: 1792
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 559 "    0.082 5.00e-02 4.00e+02   1.26e-01 2.54e+01
        pdb=" N   PRO A 560 "   -0.218 5.00e-02 4.00e+02
        pdb=" CA  PRO A 560 "    0.074 5.00e-02 4.00e+02
        pdb=" CD  PRO A 560 "    0.061 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 155 "    0.018 2.00e-02 2.50e+03   3.55e-02 1.26e+01
        pdb=" C   LYS B 155 "   -0.061 2.00e-02 2.50e+03
        pdb=" O   LYS B 155 "    0.022 2.00e-02 2.50e+03
        pdb=" N   TYR B 156 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 210 "   -0.056 5.00e-02 4.00e+02   8.47e-02 1.15e+01
        pdb=" N   PRO A 211 "    0.146 5.00e-02 4.00e+02
        pdb=" CA  PRO A 211 "   -0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO A 211 "   -0.048 5.00e-02 4.00e+02
  ... (remaining 1789 not shown)

  Histogram of nonbonded interaction distances:
        1.02 -     1.80: 6
        1.80 -     2.57: 96
        2.57 -     3.35: 13963
        3.35 -     4.12: 25650
        4.12 -     4.90: 45649
  Nonbonded interactions: 85364
  Sorted by model distance:
  nonbonded pdb=" O   ALA G  15 "
            pdb=" CB  ALA G  18 "
     model   vdw
     1.021 3.460
  nonbonded pdb=" SD  MET B 146 "
            pdb=" O   ALA G  23 "
     model   vdw
     1.099 3.400
  nonbonded pdb=" OH  TYR B 115 "
            pdb=" CA  ALA G  19 "
     model   vdw
     1.163 3.470
  nonbonded pdb=" OH  TYR B 115 "
            pdb=" N   ALA G  19 "
     model   vdw
     1.283 3.120
  nonbonded pdb=" O   ALA G  12 "
            pdb=" CB  ALA G  14 "
     model   vdw
     1.451 3.460
  ... (remaining 85359 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:             0.850
  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:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     26.120
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6251
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      :  0.011   0.100  10560  Z= 0.736
  Angle     :  1.812  15.892  14409  Z= 1.274
  Chirality :  0.102   0.602   1678
  Planarity :  0.009   0.126   1792
  Dihedral  : 18.644 117.206   3664
  Min Nonbonded Distance : 1.021

Molprobity Statistics.
  All-atom Clashscore : 20.42
  Ramachandran Plot:
    Outliers :  3.99 %
    Allowed  : 10.74 %
    Favored  : 85.28 %
  Rotamer:
    Outliers : 11.34 %
    Allowed  : 17.24 %
    Favored  : 71.42 %
  Cbeta Deviations :  2.10 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.40 %
    Twisted Proline : 3.51 %
    Twisted General : 2.07 %

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: -1.54 (0.21), residues: 1304
  helix:  1.17 (0.16), residues: 733
  sheet: -3.06 (0.39), residues: 108
  loop : -4.37 (0.22), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.004   TRP D  58 
 HIS   0.010   0.003   HIS B 214 
 PHE   0.045   0.005   PHE B 411 
 TYR   0.050   0.004   TYR C  69 
 ARG   0.006   0.001   ARG A 371 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16246 (  627)
  hydrogen bonds       : angle       6.45431 ( 1839)
  SS BOND              : bond        0.01334 (    5)
  SS BOND              : angle       1.86427 (   10)
  covalent geometry    : bond        0.01112 (10555)
  covalent geometry    : angle       1.81187 (14399)

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

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

  2608 Ramachandran restraints generated.
    1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2608 Ramachandran restraints generated.
    1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  389 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 125
    poor density    : 264
  time to evaluate  : 1.054 
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   50 CYS cc_start: 0.8638 (OUTLIER) cc_final: 0.7372 (p)
REVERT: A   95 MET cc_start: 0.9366 (mmt) cc_final: 0.8684 (mmm)
REVERT: A  312 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9122 (pp)
REVERT: A  326 MET cc_start: 0.9223 (tpt) cc_final: 0.8945 (tmm)
REVERT: A  331 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8265 (tp40)
REVERT: A  333 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8192 (mp0)
REVERT: A  443 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7375 (t0)
REVERT: A  554 TYR cc_start: 0.9302 (t80) cc_final: 0.8785 (t80)
REVERT: A  574 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8331 (mt)
REVERT: A  654 LYS cc_start: 0.9010 (pttp) cc_final: 0.8778 (ptpp)
REVERT: A  655 ASP cc_start: 0.9191 (m-30) cc_final: 0.8822 (t0)
REVERT: B   93 MET cc_start: 0.8994 (mmm) cc_final: 0.8753 (mmm)
REVERT: B  117 PRO cc_start: 0.7582 (OUTLIER) cc_final: 0.7116 (Cg_endo)
REVERT: B  184 GLU cc_start: 0.9202 (OUTLIER) cc_final: 0.8946 (mm-30)
REVERT: B  385 ASP cc_start: 0.8333 (m-30) cc_final: 0.8052 (m-30)
REVERT: B  386 PHE cc_start: 0.9085 (t80) cc_final: 0.8459 (t80)
REVERT: B  401 SER cc_start: 0.8378 (t) cc_final: 0.8125 (p)
REVERT: C   24 THR cc_start: 0.9451 (m) cc_final: 0.9240 (p)
REVERT: C  152 ASP cc_start: 0.8709 (OUTLIER) cc_final: 0.8267 (p0)
REVERT: C  178 PHE cc_start: 0.9538 (t80) cc_final: 0.9267 (t80)
REVERT: D   23 PHE cc_start: 0.8725 (m-80) cc_final: 0.8167 (m-80)
REVERT: D   39 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.7302 (tpt170)
REVERT: D   49 GLU cc_start: 0.9465 (mm-30) cc_final: 0.9056 (pt0)
REVERT: D   66 PHE cc_start: 0.9400 (t80) cc_final: 0.9174 (m-10)
REVERT: D   95 THR cc_start: 0.6596 (m) cc_final: 0.6372 (p)
  outliers start: 125
  outliers final: 30
  residues processed: 341
  average time/residue: 0.1954
  time to fit residues: 96.0621
Evaluate side-chains
  204 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 164
  time to evaluate  : 1.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 109 optimal weight:    3.9990
   chunk 98 optimal weight:    0.8980
   chunk 54 optimal weight:    6.9990
   chunk 33 optimal weight:   10.0000
   chunk 66 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 101 optimal weight:    5.9990
   chunk 39 optimal weight:    6.9990
   chunk 61 optimal weight:    4.9990
   chunk 75 optimal weight:    6.9990
   chunk 118 optimal weight:    7.9990
   overall best weight:    2.7786

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

Flipped N/Q/H residues before XYZ refinement:
A  34 ASN
A  63 GLN
A 142 ASN
** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 449 HIS
A 573 ASN
** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  68 GLN
** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  13 ASN
** D  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.051119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.043858 restraints weight = 73680.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.044892 restraints weight = 48221.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.045658 restraints weight = 33969.038|
|-----------------------------------------------------------------------------|
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.3763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  10560  Z= 0.240
  Angle     :  0.932  12.606  14409  Z= 0.487
  Chirality :  0.050   0.319   1678
  Planarity :  0.008   0.136   1792
  Dihedral  :  8.230  64.512   1416
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 17.31
  Ramachandran Plot:
    Outliers :  1.38 %
    Allowed  :  8.74 %
    Favored  : 89.88 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  5.08 %
    Favored  : 94.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.48 %
    Twisted Proline : 0.00 %
    Twisted General : 1.12 %

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 (0.24), residues: 1304
  helix:  1.75 (0.19), residues: 764
  sheet: -2.50 (0.42), residues: 124
  loop : -4.05 (0.25), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP B 247 
 HIS   0.012   0.002   HIS C 197 
 PHE   0.034   0.003   PHE A 302 
 TYR   0.047   0.003   TYR B 115 
 ARG   0.005   0.001   ARG A 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05502 (  627)
  hydrogen bonds       : angle       5.36168 ( 1839)
  SS BOND              : bond        0.01716 (    5)
  SS BOND              : angle       2.75427 (   10)
  covalent geometry    : bond        0.00494 (10555)
  covalent geometry    : angle       0.92976 (14399)

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

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

  2608 Ramachandran restraints generated.
    1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2608 Ramachandran restraints generated.
    1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 220
  time to evaluate  : 1.076 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  290 ASN cc_start: 0.9091 (t0) cc_final: 0.8600 (p0)
REVERT: A  554 TYR cc_start: 0.8668 (t80) cc_final: 0.8133 (t80)
REVERT: B  181 TYR cc_start: 0.9333 (t80) cc_final: 0.9063 (t80)
REVERT: B  233 MET cc_start: 0.8758 (ttt) cc_final: 0.8380 (ttt)
REVERT: B  385 ASP cc_start: 0.8548 (m-30) cc_final: 0.7476 (m-30)
REVERT: B  386 PHE cc_start: 0.9111 (t80) cc_final: 0.8620 (t80)
REVERT: B  388 PHE cc_start: 0.9603 (m-10) cc_final: 0.9340 (m-10)
REVERT: B  454 GLN cc_start: 0.9322 (tm-30) cc_final: 0.8878 (tm-30)
REVERT: C   41 PHE cc_start: 0.9440 (m-80) cc_final: 0.9205 (m-10)
REVERT: C   90 TYR cc_start: 0.8646 (t80) cc_final: 0.8030 (t80)
REVERT: C  132 PHE cc_start: 0.9614 (m-80) cc_final: 0.9359 (m-80)
REVERT: C  138 LEU cc_start: 0.9579 (mt) cc_final: 0.9347 (mt)
REVERT: C  152 ASP cc_start: 0.8823 (m-30) cc_final: 0.8540 (m-30)
REVERT: C  199 LEU cc_start: 0.9251 (mt) cc_final: 0.9045 (mt)
REVERT: C  204 THR cc_start: 0.9006 (p) cc_final: 0.8675 (p)
REVERT: C  218 TYR cc_start: 0.9262 (m-80) cc_final: 0.9019 (m-80)
REVERT: C  224 MET cc_start: 0.9443 (mmp) cc_final: 0.9230 (mmm)
REVERT: D   23 PHE cc_start: 0.8349 (m-80) cc_final: 0.8062 (m-80)
REVERT: D   25 PHE cc_start: 0.9232 (m-80) cc_final: 0.8962 (m-80)
REVERT: D   66 PHE cc_start: 0.9287 (t80) cc_final: 0.9019 (m-10)
  outliers start: 7
  outliers final: 0
  residues processed: 225
  average time/residue: 0.1761
  time to fit residues: 60.0064
Evaluate side-chains
  143 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 1.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 47 optimal weight:    7.9990
   chunk 93 optimal weight:    2.9990
   chunk 36 optimal weight:    9.9990
   chunk 13 optimal weight:    8.9990
   chunk 21 optimal weight:    8.9990
   chunk 39 optimal weight:    3.9990
   chunk 75 optimal weight:    4.9990
   chunk 90 optimal weight:    6.9990
   chunk 1 optimal weight:    8.9990
   chunk 71 optimal weight:   20.0000
   chunk 104 optimal weight:   10.0000
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
A  55 ASN
A 142 ASN
A 194 GLN
A 197 GLN
A 220 HIS
** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 305 GLN
A 379 HIS
A 478 ASN
A 516 GLN
A 573 ASN
** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D   8 ASN
** D  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.049163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.042362 restraints weight = 79587.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.043310 restraints weight = 52755.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.044065 restraints weight = 37939.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.4554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060  10560  Z= 0.284
  Angle     :  0.877  12.119  14409  Z= 0.459
  Chirality :  0.047   0.311   1678
  Planarity :  0.007   0.145   1792
  Dihedral  :  7.508  54.879   1416
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 19.01
  Ramachandran Plot:
    Outliers :  1.15 %
    Allowed  :  9.51 %
    Favored  : 89.34 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  3.99 %
    Favored  : 95.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.56 %
    Twisted Proline : 3.51 %
    Twisted General : 0.80 %

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: -0.88 (0.23), residues: 1304
  helix:  1.32 (0.18), residues: 754
  sheet: -2.19 (0.45), residues: 115
  loop : -3.73 (0.25), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP B 247 
 HIS   0.011   0.002   HIS C 197 
 PHE   0.033   0.003   PHE A 302 
 TYR   0.032   0.002   TYR B 115 
 ARG   0.005   0.001   ARG A 626 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04891 (  627)
  hydrogen bonds       : angle       5.36260 ( 1839)
  SS BOND              : bond        0.00841 (    5)
  SS BOND              : angle       3.30321 (   10)
  covalent geometry    : bond        0.00599 (10555)
  covalent geometry    : angle       0.87345 (14399)

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

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

  2608 Ramachandran restraints generated.
    1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2608 Ramachandran restraints generated.
    1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 175
  time to evaluate  : 1.185 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 ASN cc_start: 0.9159 (t0) cc_final: 0.8849 (t0)
REVERT: A  290 ASN cc_start: 0.9027 (t0) cc_final: 0.8632 (p0)
REVERT: A  554 TYR cc_start: 0.8657 (t80) cc_final: 0.8245 (t80)
REVERT: B   93 MET cc_start: 0.9189 (mmm) cc_final: 0.8970 (mmm)
REVERT: B  233 MET cc_start: 0.8763 (ttt) cc_final: 0.8485 (ttt)
REVERT: B  385 ASP cc_start: 0.8598 (m-30) cc_final: 0.7700 (m-30)
REVERT: B  386 PHE cc_start: 0.9044 (t80) cc_final: 0.8502 (t80)
REVERT: B  388 PHE cc_start: 0.9570 (m-10) cc_final: 0.9276 (m-10)
REVERT: B  408 ILE cc_start: 0.9657 (tp) cc_final: 0.9408 (pt)
REVERT: C   40 PHE cc_start: 0.9638 (t80) cc_final: 0.9339 (t80)
REVERT: C   41 PHE cc_start: 0.9533 (m-80) cc_final: 0.9171 (m-10)
REVERT: C   90 TYR cc_start: 0.9031 (t80) cc_final: 0.8540 (t80)
REVERT: C   99 GLU cc_start: 0.8368 (pt0) cc_final: 0.8145 (pt0)
REVERT: C  138 LEU cc_start: 0.9500 (mt) cc_final: 0.9295 (mt)
REVERT: C  178 PHE cc_start: 0.9430 (t80) cc_final: 0.9225 (t80)
REVERT: C  218 TYR cc_start: 0.9361 (m-80) cc_final: 0.9008 (m-10)
REVERT: C  224 MET cc_start: 0.9461 (mmp) cc_final: 0.9258 (mmm)
REVERT: D   23 PHE cc_start: 0.8397 (m-80) cc_final: 0.7979 (m-80)
REVERT: D   25 PHE cc_start: 0.9333 (m-80) cc_final: 0.8907 (m-80)
REVERT: D   62 VAL cc_start: 0.9607 (t) cc_final: 0.9083 (p)
REVERT: D   66 PHE cc_start: 0.9268 (t80) cc_final: 0.9025 (m-10)
REVERT: D   95 THR cc_start: 0.8251 (m) cc_final: 0.7753 (m)
  outliers start: 2
  outliers final: 1
  residues processed: 176
  average time/residue: 0.1835
  time to fit residues: 48.1291
Evaluate side-chains
  133 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 132
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 43 optimal weight:    8.9990
   chunk 119 optimal weight:   20.0000
   chunk 34 optimal weight:    8.9990
   chunk 98 optimal weight:    0.7980
   chunk 81 optimal weight:    6.9990
   chunk 75 optimal weight:    3.9990
   chunk 101 optimal weight:    7.9990
   chunk 76 optimal weight:    4.9990
   chunk 41 optimal weight:   10.0000
   chunk 44 optimal weight:    5.9990
   chunk 15 optimal weight:    3.9990
   overall best weight:    3.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 237 GLN
** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.048897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.042018 restraints weight = 74789.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.043031 restraints weight = 46691.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.043717 restraints weight = 32557.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.4957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  10560  Z= 0.219
  Angle     :  0.810  13.463  14409  Z= 0.421
  Chirality :  0.045   0.295   1678
  Planarity :  0.007   0.129   1792
  Dihedral  :  7.191  51.737   1416
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 18.53
  Ramachandran Plot:
    Outliers :  1.15 %
    Allowed  :  8.67 %
    Favored  : 90.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.56 %
    Twisted Proline : 1.75 %
    Twisted General : 0.64 %

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: -0.82 (0.23), residues: 1304
  helix:  1.29 (0.18), residues: 753
  sheet: -2.27 (0.44), residues: 117
  loop : -3.49 (0.27), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 247 
 HIS   0.010   0.002   HIS C 197 
 PHE   0.046   0.002   PHE A 210 
 TYR   0.028   0.002   TYR B 106 
 ARG   0.004   0.000   ARG B 157 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04427 (  627)
  hydrogen bonds       : angle       5.11468 ( 1839)
  SS BOND              : bond        0.00458 (    5)
  SS BOND              : angle       4.46625 (   10)
  covalent geometry    : bond        0.00458 (10555)
  covalent geometry    : angle       0.80147 (14399)

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

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

  2608 Ramachandran restraints generated.
    1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2608 Ramachandran restraints generated.
    1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 1.687 
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  290 ASN cc_start: 0.9047 (t0) cc_final: 0.8615 (p0)
REVERT: A  343 MET cc_start: 0.9327 (tpt) cc_final: 0.9118 (tpp)
REVERT: A  554 TYR cc_start: 0.8787 (t80) cc_final: 0.8577 (t80)
REVERT: B   93 MET cc_start: 0.9278 (mmt) cc_final: 0.8935 (mmp)
REVERT: B  172 LEU cc_start: 0.9512 (mm) cc_final: 0.9282 (mm)
REVERT: B  233 MET cc_start: 0.8785 (ttt) cc_final: 0.8553 (ttt)
REVERT: B  385 ASP cc_start: 0.8478 (m-30) cc_final: 0.7532 (m-30)
REVERT: B  386 PHE cc_start: 0.9108 (t80) cc_final: 0.8474 (t80)
REVERT: B  388 PHE cc_start: 0.9496 (m-10) cc_final: 0.9243 (m-10)
REVERT: B  414 ILE cc_start: 0.9136 (mt) cc_final: 0.8799 (mt)
REVERT: B  454 GLN cc_start: 0.9389 (tm-30) cc_final: 0.9157 (tm-30)
REVERT: B  466 TYR cc_start: 0.7934 (m-10) cc_final: 0.7602 (m-10)
REVERT: C   40 PHE cc_start: 0.9656 (t80) cc_final: 0.9411 (t80)
REVERT: C   41 PHE cc_start: 0.9507 (m-80) cc_final: 0.9163 (m-10)
REVERT: C   90 TYR cc_start: 0.9017 (t80) cc_final: 0.8521 (t80)
REVERT: C   99 GLU cc_start: 0.8348 (pt0) cc_final: 0.8114 (pt0)
REVERT: C  138 LEU cc_start: 0.9470 (mt) cc_final: 0.9249 (mt)
REVERT: C  178 PHE cc_start: 0.9441 (t80) cc_final: 0.9194 (t80)
REVERT: C  218 TYR cc_start: 0.9392 (m-80) cc_final: 0.9190 (m-10)
REVERT: C  224 MET cc_start: 0.9479 (mmp) cc_final: 0.9242 (mmm)
REVERT: D   23 PHE cc_start: 0.8520 (m-80) cc_final: 0.8059 (m-80)
REVERT: D   66 PHE cc_start: 0.9274 (t80) cc_final: 0.9039 (m-10)
REVERT: D   82 ARG cc_start: 0.8895 (ttp80) cc_final: 0.8561 (tpt90)
REVERT: D   95 THR cc_start: 0.8364 (m) cc_final: 0.7758 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.2270
  time to fit residues: 62.5711
Evaluate side-chains
  132 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 1.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 76 optimal weight:    8.9990
   chunk 82 optimal weight:   10.0000
   chunk 7 optimal weight:    7.9990
   chunk 29 optimal weight:    0.9980
   chunk 75 optimal weight:    3.9990
   chunk 9 optimal weight:    9.9990
   chunk 124 optimal weight:    6.9990
   chunk 45 optimal weight:    5.9990
   chunk 104 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 84 optimal weight:   20.0000
   overall best weight:    3.7586

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

Flipped N/Q/H residues before XYZ refinement:
A 313 GLN
A 449 HIS
A 573 ASN
** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  52 GLN ** 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 = 0.3149 r_free = 0.3149 target = 0.048807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.042372 restraints weight = 79272.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.043318 restraints weight = 51888.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.044008 restraints weight = 37555.762|
|-----------------------------------------------------------------------------|
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.5263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  10560  Z= 0.210
  Angle     :  0.794  14.103  14409  Z= 0.409
  Chirality :  0.044   0.297   1678
  Planarity :  0.006   0.126   1792
  Dihedral  :  6.898  50.392   1416
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 17.70
  Ramachandran Plot:
    Outliers :  1.00 %
    Allowed  :  9.05 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.56 %
    Twisted Proline : 3.51 %
    Twisted General : 0.64 %

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 (0.23), residues: 1304
  helix:  1.23 (0.18), residues: 747
  sheet: -2.02 (0.45), residues: 121
  loop : -3.22 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B 247 
 HIS   0.009   0.002   HIS C 197 
 PHE   0.022   0.002   PHE B 465 
 TYR   0.023   0.002   TYR B 106 
 ARG   0.007   0.001   ARG A 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04267 (  627)
  hydrogen bonds       : angle       5.08027 ( 1839)
  SS BOND              : bond        0.00412 (    5)
  SS BOND              : angle       3.45187 (   10)
  covalent geometry    : bond        0.00443 (10555)
  covalent geometry    : angle       0.78888 (14399)

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

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

  2608 Ramachandran restraints generated.
    1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2608 Ramachandran restraints generated.
    1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 1.145 
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  290 ASN cc_start: 0.9014 (t0) cc_final: 0.8626 (p0)
REVERT: B   93 MET cc_start: 0.9262 (mmt) cc_final: 0.8928 (mmp)
REVERT: B  182 LEU cc_start: 0.9901 (tp) cc_final: 0.9520 (pp)
REVERT: B  184 GLU cc_start: 0.9091 (mp0) cc_final: 0.8854 (mp0)
REVERT: B  233 MET cc_start: 0.8823 (ttt) cc_final: 0.8577 (ttt)
REVERT: B  385 ASP cc_start: 0.8403 (m-30) cc_final: 0.7331 (m-30)
REVERT: B  386 PHE cc_start: 0.9059 (t80) cc_final: 0.8422 (t80)
REVERT: B  388 PHE cc_start: 0.9481 (m-10) cc_final: 0.9234 (m-10)
REVERT: B  410 CYS cc_start: 0.9773 (m) cc_final: 0.9572 (m)
REVERT: B  414 ILE cc_start: 0.9237 (mt) cc_final: 0.8912 (mt)
REVERT: B  437 ILE cc_start: 0.9035 (tp) cc_final: 0.8817 (tp)
REVERT: B  445 PHE cc_start: 0.9472 (m-80) cc_final: 0.9204 (m-80)
REVERT: C   41 PHE cc_start: 0.9523 (m-80) cc_final: 0.9166 (m-10)
REVERT: C   90 TYR cc_start: 0.8988 (t80) cc_final: 0.8515 (t80)
REVERT: C   99 GLU cc_start: 0.8373 (pt0) cc_final: 0.8048 (pt0)
REVERT: C  140 ASP cc_start: 0.8869 (m-30) cc_final: 0.8661 (m-30)
REVERT: C  178 PHE cc_start: 0.9403 (t80) cc_final: 0.9160 (t80)
REVERT: C  224 MET cc_start: 0.9484 (mmp) cc_final: 0.9259 (mmm)
REVERT: D   23 PHE cc_start: 0.8481 (m-80) cc_final: 0.8025 (m-80)
REVERT: D   56 TYR cc_start: 0.8788 (m-80) cc_final: 0.8586 (m-10)
REVERT: D   66 PHE cc_start: 0.9248 (t80) cc_final: 0.8983 (m-10)
REVERT: D   95 THR cc_start: 0.8174 (m) cc_final: 0.7505 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 175
  average time/residue: 0.2373
  time to fit residues: 61.2664
Evaluate side-chains
  132 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 1.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 19 optimal weight:   10.0000
   chunk 128 optimal weight:   30.0000
   chunk 126 optimal weight:   10.0000
   chunk 77 optimal weight:    4.9990
   chunk 14 optimal weight:    6.9990
   chunk 71 optimal weight:    8.9990
   chunk 106 optimal weight:    9.9990
   chunk 40 optimal weight:    7.9990
   chunk 115 optimal weight:    0.8980
   chunk 54 optimal weight:   10.0000
   chunk 113 optimal weight:    7.9990
   overall best weight:    5.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A  63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  74 HIS
A 237 GLN
A 305 GLN
** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 573 ASN
** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  68 GLN
** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.047680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.041435 restraints weight = 82451.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.042377 restraints weight = 52796.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.042948 restraints weight = 37275.939|
|-----------------------------------------------------------------------------|
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.5576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.086  10560  Z= 0.286
  Angle     :  0.854  13.397  14409  Z= 0.445
  Chirality :  0.046   0.285   1678
  Planarity :  0.007   0.112   1792
  Dihedral  :  7.006  48.701   1416
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 21.92
  Ramachandran Plot:
    Outliers :  0.92 %
    Allowed  :  9.20 %
    Favored  : 89.88 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  3.63 %
    Favored  : 96.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.56 %
    Twisted Proline : 3.51 %
    Twisted General : 0.56 %

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: -1.05 (0.23), residues: 1304
  helix:  0.92 (0.18), residues: 746
  sheet: -2.12 (0.43), residues: 116
  loop : -3.21 (0.27), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP D  36 
 HIS   0.017   0.003   HIS C 197 
 PHE   0.022   0.003   PHE B  86 
 TYR   0.027   0.002   TYR B 466 
 ARG   0.006   0.001   ARG A 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04543 (  627)
  hydrogen bonds       : angle       5.26819 ( 1839)
  SS BOND              : bond        0.00805 (    5)
  SS BOND              : angle       4.64294 (   10)
  covalent geometry    : bond        0.00596 (10555)
  covalent geometry    : angle       0.84517 (14399)

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

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

  2608 Ramachandran restraints generated.
    1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2608 Ramachandran restraints generated.
    1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 172
  time to evaluate  : 1.099 
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  290 ASN cc_start: 0.9088 (t0) cc_final: 0.8484 (t0)
REVERT: B   93 MET cc_start: 0.9327 (mmt) cc_final: 0.8947 (mmm)
REVERT: B  172 LEU cc_start: 0.9612 (mm) cc_final: 0.9366 (mm)
REVERT: B  195 TYR cc_start: 0.9039 (m-80) cc_final: 0.8781 (m-10)
REVERT: B  233 MET cc_start: 0.8827 (ttt) cc_final: 0.8605 (ttt)
REVERT: B  385 ASP cc_start: 0.8525 (m-30) cc_final: 0.7642 (m-30)
REVERT: B  386 PHE cc_start: 0.9075 (t80) cc_final: 0.8501 (t80)
REVERT: B  388 PHE cc_start: 0.9404 (m-10) cc_final: 0.8992 (m-10)
REVERT: B  414 ILE cc_start: 0.9212 (mt) cc_final: 0.8911 (mt)
REVERT: B  445 PHE cc_start: 0.9437 (m-80) cc_final: 0.9050 (m-80)
REVERT: B  466 TYR cc_start: 0.7788 (m-80) cc_final: 0.7421 (m-10)
REVERT: C   40 PHE cc_start: 0.9621 (t80) cc_final: 0.9368 (t80)
REVERT: C   41 PHE cc_start: 0.9535 (m-80) cc_final: 0.9139 (m-10)
REVERT: C   90 TYR cc_start: 0.9013 (t80) cc_final: 0.8548 (t80)
REVERT: C   99 GLU cc_start: 0.8333 (pt0) cc_final: 0.8099 (pt0)
REVERT: C  178 PHE cc_start: 0.9401 (t80) cc_final: 0.9070 (t80)
REVERT: C  224 MET cc_start: 0.9510 (mmp) cc_final: 0.9225 (mmm)
REVERT: D   23 PHE cc_start: 0.8630 (m-80) cc_final: 0.8077 (m-80)
REVERT: D   56 TYR cc_start: 0.8891 (m-80) cc_final: 0.8566 (m-10)
REVERT: D   66 PHE cc_start: 0.9277 (t80) cc_final: 0.9036 (m-10)
REVERT: D   95 THR cc_start: 0.8314 (m) cc_final: 0.7729 (m)
  outliers start: 2
  outliers final: 1
  residues processed: 173
  average time/residue: 0.2028
  time to fit residues: 53.0394
Evaluate side-chains
  130 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 129
  time to evaluate  : 1.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 91 optimal weight:    0.9990
   chunk 59 optimal weight:    0.2980
   chunk 113 optimal weight:    9.9990
   chunk 114 optimal weight:    0.8980
   chunk 109 optimal weight:    6.9990
   chunk 126 optimal weight:    9.9990
   chunk 22 optimal weight:    8.9990
   chunk 29 optimal weight:    0.9990
   chunk 51 optimal weight:    6.9990
   chunk 23 optimal weight:    7.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    1.0386

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

Flipped N/Q/H residues before XYZ refinement:
A 531 ASN
A 606 GLN
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 222 GLN
** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 171 HIS
** D  13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.050519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.043867 restraints weight = 80161.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.044899 restraints weight = 51931.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.045657 restraints weight = 37192.142|
|-----------------------------------------------------------------------------|
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.5896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  10560  Z= 0.150
  Angle     :  0.807  17.562  14409  Z= 0.406
  Chirality :  0.045   0.342   1678
  Planarity :  0.007   0.161   1792
  Dihedral  :  6.579  46.813   1416
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 15.57
  Ramachandran Plot:
    Outliers :  0.92 %
    Allowed  :  7.82 %
    Favored  : 91.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.48 %
    Twisted Proline : 1.75 %
    Twisted General : 0.48 %

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: -0.63 (0.24), residues: 1304
  helix:  1.23 (0.18), residues: 747
  sheet: -1.99 (0.44), residues: 119
  loop : -2.97 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 247 
 HIS   0.009   0.001   HIS C 171 
 PHE   0.027   0.002   PHE A 210 
 TYR   0.030   0.002   TYR D  18 
 ARG   0.008   0.001   ARG B 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04101 (  627)
  hydrogen bonds       : angle       4.96572 ( 1839)
  SS BOND              : bond        0.01213 (    5)
  SS BOND              : angle       5.31015 (   10)
  covalent geometry    : bond        0.00322 (10555)
  covalent geometry    : angle       0.79533 (14399)

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

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

  2608 Ramachandran restraints generated.
    1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2608 Ramachandran restraints generated.
    1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 1.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  215 MET cc_start: 0.9194 (mtm) cc_final: 0.8878 (mmm)
REVERT: A  290 ASN cc_start: 0.9189 (t0) cc_final: 0.8526 (t0)
REVERT: B   93 MET cc_start: 0.9265 (mmt) cc_final: 0.8875 (mmm)
REVERT: B  106 TYR cc_start: 0.8748 (m-10) cc_final: 0.8498 (m-10)
REVERT: B  172 LEU cc_start: 0.9573 (mm) cc_final: 0.9320 (mm)
REVERT: B  176 PHE cc_start: 0.9159 (t80) cc_final: 0.8826 (t80)
REVERT: B  233 MET cc_start: 0.8746 (ttt) cc_final: 0.8513 (ttt)
REVERT: B  385 ASP cc_start: 0.8256 (m-30) cc_final: 0.7083 (m-30)
REVERT: B  386 PHE cc_start: 0.9024 (t80) cc_final: 0.8459 (t80)
REVERT: B  388 PHE cc_start: 0.9336 (m-10) cc_final: 0.8978 (m-10)
REVERT: B  410 CYS cc_start: 0.9744 (m) cc_final: 0.9522 (m)
REVERT: B  414 ILE cc_start: 0.9153 (mt) cc_final: 0.8836 (mt)
REVERT: B  445 PHE cc_start: 0.9410 (m-80) cc_final: 0.9024 (m-80)
REVERT: B  454 GLN cc_start: 0.9259 (tm-30) cc_final: 0.8954 (tm-30)
REVERT: C   35 LEU cc_start: 0.9576 (tt) cc_final: 0.9361 (mm)
REVERT: C   40 PHE cc_start: 0.9561 (t80) cc_final: 0.9321 (t80)
REVERT: C   41 PHE cc_start: 0.9494 (m-80) cc_final: 0.9072 (m-10)
REVERT: C   90 TYR cc_start: 0.8761 (t80) cc_final: 0.8310 (t80)
REVERT: C   99 GLU cc_start: 0.8307 (pt0) cc_final: 0.7999 (pt0)
REVERT: C  119 TYR cc_start: 0.8917 (t80) cc_final: 0.8576 (t80)
REVERT: C  224 MET cc_start: 0.9467 (mmp) cc_final: 0.9245 (mmm)
REVERT: D   23 PHE cc_start: 0.8631 (m-80) cc_final: 0.8115 (m-80)
REVERT: D   66 PHE cc_start: 0.9247 (t80) cc_final: 0.8992 (m-10)
REVERT: D   95 THR cc_start: 0.8146 (m) cc_final: 0.7713 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 190
  average time/residue: 0.1840
  time to fit residues: 52.4463
Evaluate side-chains
  141 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 1.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 83 optimal weight:    9.9990
   chunk 106 optimal weight:    5.9990
   chunk 86 optimal weight:    9.9990
   chunk 67 optimal weight:    2.9990
   chunk 75 optimal weight:    0.6980
   chunk 33 optimal weight:    7.9990
   chunk 47 optimal weight:   20.0000
   chunk 17 optimal weight:    4.9990
   chunk 25 optimal weight:    8.9990
   chunk 118 optimal weight:    2.9990
   chunk 68 optimal weight:    5.9990
   overall best weight:    3.5388

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

Flipped N/Q/H residues before XYZ refinement:
A 573 ASN
A 610 HIS
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 459 GLN
** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  52 GLN ** 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 = 0.3165 r_free = 0.3165 target = 0.048868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.042425 restraints weight = 80875.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.043363 restraints weight = 51594.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.043993 restraints weight = 37242.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.6110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077  10560  Z= 0.208
  Angle     :  0.805  17.632  14409  Z= 0.413
  Chirality :  0.045   0.278   1678
  Planarity :  0.007   0.143   1792
  Dihedral  :  6.531  46.061   1416
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 18.24
  Ramachandran Plot:
    Outliers :  0.92 %
    Allowed  :  8.59 %
    Favored  : 90.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.56 %
    Twisted Proline : 1.75 %
    Twisted General : 0.32 %

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: -0.75 (0.23), residues: 1304
  helix:  1.09 (0.18), residues: 754
  sheet: -1.98 (0.44), residues: 118
  loop : -3.03 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 247 
 HIS   0.009   0.002   HIS C  58 
 PHE   0.032   0.002   PHE A 682 
 TYR   0.022   0.002   TYR C 119 
 ARG   0.006   0.001   ARG B 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04262 (  627)
  hydrogen bonds       : angle       5.09501 ( 1839)
  SS BOND              : bond        0.01142 (    5)
  SS BOND              : angle       6.36157 (   10)
  covalent geometry    : bond        0.00440 (10555)
  covalent geometry    : angle       0.78719 (14399)

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

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

  2608 Ramachandran restraints generated.
    1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2608 Ramachandran restraints generated.
    1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 1.140 
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   46 LYS cc_start: 0.9261 (tttm) cc_final: 0.8817 (tmtt)
REVERT: A  213 CYS cc_start: 0.3180 (p) cc_final: 0.2964 (p)
REVERT: A  290 ASN cc_start: 0.9152 (t0) cc_final: 0.8564 (t0)
REVERT: A  682 PHE cc_start: 0.9292 (m-80) cc_final: 0.9085 (m-10)
REVERT: B   84 MET cc_start: 0.9168 (ptp) cc_final: 0.8962 (ptt)
REVERT: B   93 MET cc_start: 0.9339 (mmt) cc_final: 0.8996 (mmp)
REVERT: B  106 TYR cc_start: 0.8850 (m-10) cc_final: 0.8622 (m-10)
REVERT: B  172 LEU cc_start: 0.9591 (mm) cc_final: 0.9336 (mm)
REVERT: B  177 PHE cc_start: 0.9462 (m-80) cc_final: 0.9219 (m-80)
REVERT: B  233 MET cc_start: 0.8829 (ttt) cc_final: 0.8586 (ttt)
REVERT: B  385 ASP cc_start: 0.8284 (m-30) cc_final: 0.7116 (m-30)
REVERT: B  386 PHE cc_start: 0.9014 (t80) cc_final: 0.8517 (t80)
REVERT: B  388 PHE cc_start: 0.9323 (m-10) cc_final: 0.8868 (m-10)
REVERT: B  414 ILE cc_start: 0.9198 (mt) cc_final: 0.8899 (mt)
REVERT: B  445 PHE cc_start: 0.9436 (m-80) cc_final: 0.9043 (m-80)
REVERT: C   40 PHE cc_start: 0.9631 (t80) cc_final: 0.9411 (t80)
REVERT: C   41 PHE cc_start: 0.9485 (m-80) cc_final: 0.9060 (m-10)
REVERT: C   90 TYR cc_start: 0.8933 (t80) cc_final: 0.8421 (t80)
REVERT: C   99 GLU cc_start: 0.8327 (pt0) cc_final: 0.7896 (pt0)
REVERT: C  224 MET cc_start: 0.9517 (mmp) cc_final: 0.9243 (mmm)
REVERT: D   23 PHE cc_start: 0.8668 (m-80) cc_final: 0.8102 (m-80)
REVERT: D   56 TYR cc_start: 0.8834 (m-80) cc_final: 0.8574 (m-10)
REVERT: D   66 PHE cc_start: 0.9318 (t80) cc_final: 0.9043 (m-10)
REVERT: D   95 THR cc_start: 0.8192 (m) cc_final: 0.7461 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 171
  average time/residue: 0.2148
  time to fit residues: 56.5077
Evaluate side-chains
  127 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 1.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 45 optimal weight:    6.9990
   chunk 72 optimal weight:    6.9990
   chunk 58 optimal weight:    6.9990
   chunk 94 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 89 optimal weight:    8.9990
   chunk 109 optimal weight:    0.0970
   chunk 98 optimal weight:    9.9990
   chunk 25 optimal weight:    0.4980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 562 ASN
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.050477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.043899 restraints weight = 78082.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.044898 restraints weight = 50678.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.045624 restraints weight = 36029.876|
|-----------------------------------------------------------------------------|
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.6295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076  10560  Z= 0.155
  Angle     :  0.815  19.264  14409  Z= 0.412
  Chirality :  0.045   0.288   1678
  Planarity :  0.006   0.132   1792
  Dihedral  :  6.299  45.010   1416
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 17.22
  Ramachandran Plot:
    Outliers :  1.00 %
    Allowed  :  8.13 %
    Favored  : 90.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.48 %
    Twisted Proline : 1.75 %
    Twisted General : 0.40 %

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: -0.67 (0.23), residues: 1304
  helix:  1.09 (0.18), residues: 757
  sheet: -1.87 (0.43), residues: 118
  loop : -2.89 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP D  74 
 HIS   0.012   0.001   HIS C 171 
 PHE   0.048   0.002   PHE C 205 
 TYR   0.027   0.002   TYR C 119 
 ARG   0.006   0.001   ARG A 117 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04197 (  627)
  hydrogen bonds       : angle       5.05553 ( 1839)
  SS BOND              : bond        0.01294 (    5)
  SS BOND              : angle       6.77464 (   10)
  covalent geometry    : bond        0.00339 (10555)
  covalent geometry    : angle       0.79589 (14399)

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

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

  2608 Ramachandran restraints generated.
    1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2608 Ramachandran restraints generated.
    1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 1.150 
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  290 ASN cc_start: 0.9211 (t0) cc_final: 0.8718 (t0)
REVERT: A  347 MET cc_start: 0.9255 (tpp) cc_final: 0.8941 (tpp)
REVERT: A  682 PHE cc_start: 0.9313 (m-80) cc_final: 0.9067 (m-10)
REVERT: B   93 MET cc_start: 0.9317 (mmt) cc_final: 0.8979 (mmp)
REVERT: B  106 TYR cc_start: 0.8873 (m-10) cc_final: 0.8237 (m-10)
REVERT: B  168 ILE cc_start: 0.9380 (mm) cc_final: 0.9069 (mt)
REVERT: B  172 LEU cc_start: 0.9633 (mm) cc_final: 0.9316 (mm)
REVERT: B  176 PHE cc_start: 0.9155 (t80) cc_final: 0.8811 (t80)
REVERT: B  177 PHE cc_start: 0.9470 (m-80) cc_final: 0.8988 (m-80)
REVERT: B  181 TYR cc_start: 0.9190 (t80) cc_final: 0.8958 (t80)
REVERT: B  184 GLU cc_start: 0.9338 (mp0) cc_final: 0.8645 (mp0)
REVERT: B  211 ILE cc_start: 0.9578 (tp) cc_final: 0.9192 (tp)
REVERT: B  233 MET cc_start: 0.8793 (ttt) cc_final: 0.8546 (ttt)
REVERT: B  385 ASP cc_start: 0.8213 (m-30) cc_final: 0.7867 (p0)
REVERT: B  386 PHE cc_start: 0.9042 (t80) cc_final: 0.8690 (t80)
REVERT: B  388 PHE cc_start: 0.9292 (m-10) cc_final: 0.9023 (m-10)
REVERT: B  414 ILE cc_start: 0.9134 (mt) cc_final: 0.8836 (mt)
REVERT: B  445 PHE cc_start: 0.9460 (m-80) cc_final: 0.9070 (m-80)
REVERT: B  454 GLN cc_start: 0.9217 (tm-30) cc_final: 0.8979 (tm-30)
REVERT: C   40 PHE cc_start: 0.9609 (t80) cc_final: 0.9398 (t80)
REVERT: C   41 PHE cc_start: 0.9391 (m-80) cc_final: 0.9034 (m-10)
REVERT: C   90 TYR cc_start: 0.8861 (t80) cc_final: 0.8414 (t80)
REVERT: C   99 GLU cc_start: 0.8301 (pt0) cc_final: 0.7869 (pt0)
REVERT: C  211 GLU cc_start: 0.6599 (tm-30) cc_final: 0.6372 (tm-30)
REVERT: C  224 MET cc_start: 0.9482 (mmp) cc_final: 0.9209 (mmm)
REVERT: D   23 PHE cc_start: 0.8677 (m-80) cc_final: 0.8121 (m-80)
REVERT: D   66 PHE cc_start: 0.9253 (t80) cc_final: 0.9050 (m-10)
REVERT: D   95 THR cc_start: 0.8030 (m) cc_final: 0.7353 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 181
  average time/residue: 0.2266
  time to fit residues: 63.1483
Evaluate side-chains
  142 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 2.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 101 optimal weight:    9.9990
   chunk 65 optimal weight:    3.9990
   chunk 92 optimal weight:   10.0000
   chunk 109 optimal weight:    0.9980
   chunk 76 optimal weight:    5.9990
   chunk 110 optimal weight:    5.9990
   chunk 49 optimal weight:    9.9990
   chunk 100 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 116 optimal weight:    3.9990
   chunk 69 optimal weight:   20.0000
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 199 HIS
A 454 GLN
A 573 ASN
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  52 GLN ** 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 = 0.3196 r_free = 0.3196 target = 0.049676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.043204 restraints weight = 77925.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.044202 restraints weight = 51013.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.044905 restraints weight = 36416.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.6446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  10560  Z= 0.167
  Angle     :  0.785  13.279  14409  Z= 0.397
  Chirality :  0.044   0.278   1678
  Planarity :  0.006   0.128   1792
  Dihedral  :  6.197  44.405   1416
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 17.31
  Ramachandran Plot:
    Outliers :  0.84 %
    Allowed  :  8.44 %
    Favored  : 90.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.56 %
    Twisted Proline : 1.75 %
    Twisted General : 0.40 %

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: -0.60 (0.24), residues: 1304
  helix:  1.18 (0.18), residues: 756
  sheet: -2.10 (0.41), residues: 121
  loop : -2.84 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B 247 
 HIS   0.007   0.001   HIS C  58 
 PHE   0.021   0.002   PHE A 682 
 TYR   0.021   0.002   TYR C 119 
 ARG   0.006   0.001   ARG B 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04013 (  627)
  hydrogen bonds       : angle       5.01747 ( 1839)
  SS BOND              : bond        0.01123 (    5)
  SS BOND              : angle       2.61922 (   10)
  covalent geometry    : bond        0.00360 (10555)
  covalent geometry    : angle       0.78251 (14399)

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

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

  2608 Ramachandran restraints generated.
    1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2608 Ramachandran restraints generated.
    1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 1.701 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  290 ASN cc_start: 0.9201 (t0) cc_final: 0.8691 (t0)
REVERT: A  305 GLN cc_start: 0.9302 (tp-100) cc_final: 0.9080 (tp40)
REVERT: A  347 MET cc_start: 0.9294 (tpp) cc_final: 0.8925 (tpp)
REVERT: A  682 PHE cc_start: 0.9330 (m-80) cc_final: 0.9040 (m-10)
REVERT: B   93 MET cc_start: 0.9316 (mmt) cc_final: 0.9056 (mmp)
REVERT: B  106 TYR cc_start: 0.8873 (m-10) cc_final: 0.8189 (m-10)
REVERT: B  168 ILE cc_start: 0.9369 (mm) cc_final: 0.9166 (mt)
REVERT: B  172 LEU cc_start: 0.9570 (mm) cc_final: 0.9370 (mm)
REVERT: B  176 PHE cc_start: 0.9141 (t80) cc_final: 0.8804 (t80)
REVERT: B  177 PHE cc_start: 0.9458 (m-80) cc_final: 0.9004 (m-80)
REVERT: B  184 GLU cc_start: 0.9310 (mp0) cc_final: 0.8632 (mp0)
REVERT: B  210 MET cc_start: 0.8335 (ppp) cc_final: 0.8023 (ppp)
REVERT: B  385 ASP cc_start: 0.8248 (m-30) cc_final: 0.7898 (p0)
REVERT: B  386 PHE cc_start: 0.9026 (t80) cc_final: 0.8719 (t80)
REVERT: B  388 PHE cc_start: 0.9304 (m-10) cc_final: 0.9008 (m-10)
REVERT: B  414 ILE cc_start: 0.9171 (mt) cc_final: 0.8884 (mt)
REVERT: B  445 PHE cc_start: 0.9457 (m-80) cc_final: 0.9104 (m-80)
REVERT: B  454 GLN cc_start: 0.9251 (tm-30) cc_final: 0.8991 (tm-30)
REVERT: B  463 HIS cc_start: 0.8925 (m90) cc_final: 0.8604 (m-70)
REVERT: C   40 PHE cc_start: 0.9630 (t80) cc_final: 0.9406 (t80)
REVERT: C   41 PHE cc_start: 0.9454 (m-80) cc_final: 0.9071 (m-10)
REVERT: C   90 TYR cc_start: 0.8935 (t80) cc_final: 0.8353 (t80)
REVERT: C   99 GLU cc_start: 0.8299 (pt0) cc_final: 0.7857 (pt0)
REVERT: C  128 ILE cc_start: 0.9241 (tp) cc_final: 0.8996 (tp)
REVERT: C  132 PHE cc_start: 0.8580 (m-80) cc_final: 0.8134 (m-80)
REVERT: C  224 MET cc_start: 0.9516 (mmp) cc_final: 0.9171 (mmm)
REVERT: D   23 PHE cc_start: 0.8662 (m-80) cc_final: 0.8143 (m-80)
REVERT: D   56 TYR cc_start: 0.8982 (m-80) cc_final: 0.8777 (m-80)
REVERT: D   66 PHE cc_start: 0.9313 (t80) cc_final: 0.9018 (m-10)
REVERT: D   95 THR cc_start: 0.8033 (m) cc_final: 0.7328 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 175
  average time/residue: 0.2102
  time to fit residues: 55.3350
Evaluate side-chains
  135 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 1.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 108 optimal weight:    0.0050
   chunk 101 optimal weight:    4.9990
   chunk 53 optimal weight:    9.9990
   chunk 4 optimal weight:    3.9990
   chunk 95 optimal weight:   10.0000
   chunk 42 optimal weight:   10.0000
   chunk 54 optimal weight:   10.0000
   chunk 59 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9980
   chunk 107 optimal weight:    1.9990
   overall best weight:    0.9396

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

Flipped N/Q/H residues before XYZ refinement:
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  83 GLN
** D  13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.050634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.044056 restraints weight = 78512.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.045075 restraints weight = 51231.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.045829 restraints weight = 36520.331|
|-----------------------------------------------------------------------------|
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.6590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  10560  Z= 0.148
  Angle     :  0.794  12.428  14409  Z= 0.398
  Chirality :  0.044   0.279   1678
  Planarity :  0.006   0.124   1792
  Dihedral  :  6.125  44.380   1416
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 16.93
  Ramachandran Plot:
    Outliers :  0.84 %
    Allowed  :  8.36 %
    Favored  : 90.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.56 %
    Twisted Proline : 3.51 %
    Twisted General : 0.24 %

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: -0.66 (0.24), residues: 1304
  helix:  1.10 (0.18), residues: 752
  sheet: -2.06 (0.41), residues: 123
  loop : -2.80 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP C 174 
 HIS   0.006   0.001   HIS C 197 
 PHE   0.020   0.002   PHE A 302 
 TYR   0.022   0.002   TYR A 554 
 ARG   0.014   0.001   ARG A 117 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03993 (  627)
  hydrogen bonds       : angle       4.95061 ( 1839)
  SS BOND              : bond        0.00749 (    5)
  SS BOND              : angle       2.11780 (   10)
  covalent geometry    : bond        0.00322 (10555)
  covalent geometry    : angle       0.79239 (14399)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3213.04 seconds
wall clock time: 60 minutes 10.91 seconds (3610.91 seconds total)