Starting phenix.real_space_refine
on Wed Sep 17 18:14:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5fn3_3238/09_2025/5fn3_3238.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5fn3_3238/09_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_3238/09_2025/5fn3_3238.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5fn3_3238/09_2025/5fn3_3238.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5fn3_3238/09_2025/5fn3_3238.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5fn3_3238/09_2025/5fn3_3238.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: {'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1, 'TYR: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: 2.42, per 1000 atoms: 0.24
  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: 1.05
  Conformation dependent library (CDL) restraints added in 416.1 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.35
  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: 1.51

  Time building geometry restraints manager: 1.36 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:             0.500
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.800
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.880
-------------------------------------------------------------------------------
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 : 20.52
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.54 (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
 ARG   0.006   0.001   ARG A 371 
 TYR   0.050   0.004   TYR C  69 
 PHE   0.045   0.005   PHE B 411 
 TRP   0.026   0.004   TRP D  58 
 HIS   0.010   0.003   HIS B 214 

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

*********************** 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  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   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: 0.9123 (pp)
REVERT: A  326 MET cc_start: 0.9223 (tpt) cc_final: 0.8946 (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: 0.8330 (mt)
REVERT: A  637 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8765 (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: 0.8823 (t0)
REVERT: B   93 MET cc_start: 0.8994 (mmm) cc_final: 0.8750 (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: 0.8044 (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: B  410 CYS cc_start: 0.9554 (m) cc_final: 0.9348 (m)
REVERT: C   24 THR cc_start: 0.9451 (m) cc_final: 0.9239 (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: 0.9303 (t80)
REVERT: D   17 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7961 (mttt)
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: 0.9062 (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: 0.0933
  time to fit residues: 46.3894
Evaluate side-chains
  209 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 167
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    7.9990
   chunk 66 optimal weight:    2.9990
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:    7.9990
   chunk 55 optimal weight:    0.7980
   chunk 129 optimal weight:    6.9990
   overall best weight:    3.1386

-------------------------------------------------------------------------------
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 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 194 GLN
** 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 405 ASN
** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  68 GLN
C 136 ASN
** 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: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.050874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.043714 restraints weight = 73039.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.044768 restraints weight = 46948.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.045337 restraints weight = 33418.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.045874 restraints weight = 27012.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.046371 restraints weight = 22699.429|
|-----------------------------------------------------------------------------|
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.3778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.074  10560  Z= 0.236
  Angle     :  0.925  13.087  14409  Z= 0.483
  Chirality :  0.049   0.309   1678
  Planarity :  0.008   0.133   1792
  Dihedral  :  8.181  63.284   1416
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 17.70
  Ramachandran Plot:
    Outliers :  1.46 %
    Allowed  :  8.74 %
    Favored  : 89.80 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  5.26 %
    Favored  : 94.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.48 %
    Twisted Proline : 0.00 %
    Twisted General : 1.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.50 (0.24), residues: 1304
  helix:  1.85 (0.19), residues: 754
  sheet: -2.49 (0.42), residues: 124
  loop : -3.91 (0.25), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 232 
 TYR   0.044   0.003   TYR B 115 
 PHE   0.033   0.003   PHE A 302 
 TRP   0.036   0.002   TRP B 247 
 HIS   0.013   0.002   HIS C 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00513 (10555)
  covalent geometry    : angle       0.92336 (14399)
  SS BOND              : bond        0.01016 (    5)
  SS BOND              : angle       2.48602 (   10)
  hydrogen bonds       : bond        0.05368 (  627)
  hydrogen bonds       : angle       5.35332 ( 1839)

*********************** 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  : 0.393 
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  290 ASN cc_start: 0.9098 (t0) cc_final: 0.8583 (p0)
REVERT: A  554 TYR cc_start: 0.8640 (t80) cc_final: 0.8113 (t80)
REVERT: B  177 PHE cc_start: 0.8999 (m-80) cc_final: 0.8778 (m-80)
REVERT: B  181 TYR cc_start: 0.9331 (t80) cc_final: 0.8962 (t80)
REVERT: B  184 GLU cc_start: 0.9155 (mp0) cc_final: 0.8931 (mp0)
REVERT: B  233 MET cc_start: 0.8717 (ttt) cc_final: 0.8323 (ttt)
REVERT: B  385 ASP cc_start: 0.8588 (m-30) cc_final: 0.7624 (m-30)
REVERT: B  386 PHE cc_start: 0.9077 (t80) cc_final: 0.8557 (t80)
REVERT: B  388 PHE cc_start: 0.9593 (m-10) cc_final: 0.9331 (m-10)
REVERT: B  454 GLN cc_start: 0.9328 (tm-30) cc_final: 0.8978 (tm-30)
REVERT: C   41 PHE cc_start: 0.9442 (m-80) cc_final: 0.9198 (m-10)
REVERT: C   90 TYR cc_start: 0.8629 (t80) cc_final: 0.8000 (t80)
REVERT: C  138 LEU cc_start: 0.9583 (mt) cc_final: 0.9352 (mt)
REVERT: C  152 ASP cc_start: 0.8793 (m-30) cc_final: 0.8514 (m-30)
REVERT: C  218 TYR cc_start: 0.9239 (m-80) cc_final: 0.9032 (m-80)
REVERT: C  224 MET cc_start: 0.9461 (mmp) cc_final: 0.9240 (mmm)
REVERT: D   23 PHE cc_start: 0.8307 (m-80) cc_final: 0.8045 (m-80)
REVERT: D   25 PHE cc_start: 0.9196 (m-80) cc_final: 0.8948 (m-80)
REVERT: D   66 PHE cc_start: 0.9230 (t80) cc_final: 0.9002 (m-10)
  outliers start: 7
  outliers final: 0
  residues processed: 225
  average time/residue: 0.0808
  time to fit residues: 27.9922
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  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 32 optimal weight:    9.9990
   chunk 25 optimal weight:    6.9990
   chunk 88 optimal weight:   10.0000
   chunk 53 optimal weight:    9.9990
   chunk 48 optimal weight:    1.9990
   chunk 105 optimal weight:    0.9980
   chunk 41 optimal weight:    8.9990
   chunk 111 optimal weight:   10.0000
   chunk 4 optimal weight:    5.9990
   chunk 70 optimal weight:    8.9990
   chunk 64 optimal weight:    8.9990
   overall best weight:    4.9988

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

Flipped N/Q/H residues before XYZ refinement:
A  55 ASN
A 197 GLN
A 220 HIS
** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 305 GLN
** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
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 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3143 r_free = 0.3143 target = 0.048716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.041791 restraints weight = 75936.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.042792 restraints weight = 49386.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.043525 restraints weight = 34702.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.044000 restraints weight = 27545.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.044396 restraints weight = 23060.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.4579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  10560  Z= 0.267
  Angle     :  0.860  12.063  14409  Z= 0.449
  Chirality :  0.047   0.352   1678
  Planarity :  0.007   0.145   1792
  Dihedral  :  7.420  54.217   1416
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 18.82
  Ramachandran Plot:
    Outliers :  1.07 %
    Allowed  :  9.43 %
    Favored  : 89.49 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  4.17 %
    Favored  : 95.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.56 %
    Twisted Proline : 3.51 %
    Twisted General : 0.72 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.85 (0.23), residues: 1304
  helix:  1.31 (0.18), residues: 761
  sheet: -2.23 (0.44), residues: 115
  loop : -3.71 (0.26), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 220 
 TYR   0.029   0.002   TYR B 115 
 PHE   0.031   0.003   PHE A 181 
 TRP   0.045   0.002   TRP B 247 
 HIS   0.016   0.002   HIS C 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00560 (10555)
  covalent geometry    : angle       0.85665 (14399)
  SS BOND              : bond        0.01125 (    5)
  SS BOND              : angle       2.91782 (   10)
  hydrogen bonds       : bond        0.04890 (  627)
  hydrogen bonds       : angle       5.33680 ( 1839)

*********************** 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
  180 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 178
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  221 MET cc_start: 0.9279 (mmp) cc_final: 0.8969 (mmp)
REVERT: A  243 ASN cc_start: 0.9178 (t0) cc_final: 0.8869 (t0)
REVERT: A  290 ASN cc_start: 0.9098 (t0) cc_final: 0.8576 (p0)
REVERT: A  343 MET cc_start: 0.9331 (tpt) cc_final: 0.9111 (tpp)
REVERT: A  554 TYR cc_start: 0.8686 (t80) cc_final: 0.8229 (t80)
REVERT: B   93 MET cc_start: 0.9190 (mmm) cc_final: 0.8899 (mmm)
REVERT: B  177 PHE cc_start: 0.9177 (m-80) cc_final: 0.8830 (m-80)
REVERT: B  182 LEU cc_start: 0.9912 (tp) cc_final: 0.9554 (pp)
REVERT: B  233 MET cc_start: 0.8845 (ttt) cc_final: 0.8562 (ttt)
REVERT: B  385 ASP cc_start: 0.8522 (m-30) cc_final: 0.7554 (m-30)
REVERT: B  386 PHE cc_start: 0.9001 (t80) cc_final: 0.8415 (t80)
REVERT: B  388 PHE cc_start: 0.9548 (m-10) cc_final: 0.9264 (m-10)
REVERT: C   40 PHE cc_start: 0.9644 (t80) cc_final: 0.9378 (t80)
REVERT: C   41 PHE cc_start: 0.9517 (m-80) cc_final: 0.9149 (m-10)
REVERT: C   90 TYR cc_start: 0.9076 (t80) cc_final: 0.8512 (t80)
REVERT: C   99 GLU cc_start: 0.8432 (pt0) cc_final: 0.8192 (pt0)
REVERT: C  138 LEU cc_start: 0.9469 (mt) cc_final: 0.9265 (mt)
REVERT: C  178 PHE cc_start: 0.9465 (t80) cc_final: 0.9223 (t80)
REVERT: C  218 TYR cc_start: 0.9368 (m-80) cc_final: 0.9096 (m-10)
REVERT: C  224 MET cc_start: 0.9469 (mmp) cc_final: 0.9185 (mmm)
REVERT: D   18 TYR cc_start: 0.8787 (m-80) cc_final: 0.8540 (m-80)
REVERT: D   23 PHE cc_start: 0.8419 (m-80) cc_final: 0.7995 (m-80)
REVERT: D   25 PHE cc_start: 0.9313 (m-80) cc_final: 0.8901 (m-80)
REVERT: D   62 VAL cc_start: 0.9605 (t) cc_final: 0.9169 (p)
REVERT: D   66 PHE cc_start: 0.9271 (t80) cc_final: 0.9036 (m-10)
REVERT: D   95 THR cc_start: 0.8255 (m) cc_final: 0.7734 (m)
  outliers start: 2
  outliers final: 1
  residues processed: 179
  average time/residue: 0.0900
  time to fit residues: 24.1211
Evaluate side-chains
  132 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 131
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 3 optimal weight:    9.9990
   chunk 85 optimal weight:    0.0010
   chunk 117 optimal weight:    4.9990
   chunk 122 optimal weight:    3.9990
   chunk 64 optimal weight:   10.0000
   chunk 46 optimal weight:   10.0000
   chunk 9 optimal weight:    0.0070
   chunk 34 optimal weight:    9.9990
   chunk 95 optimal weight:    8.9990
   chunk 17 optimal weight:    3.9990
   overall best weight:    2.6010

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

Flipped N/Q/H residues before XYZ refinement:
A 237 GLN
A 305 GLN
A 449 HIS
A 573 ASN
A 606 GLN
** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 136 ASN ** 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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.050317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.043245 restraints weight = 79341.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.044350 restraints weight = 51214.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.045047 restraints weight = 35283.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.045626 restraints weight = 27830.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.045981 restraints weight = 22237.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.4952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10560  Z= 0.178
  Angle     :  0.790  13.416  14409  Z= 0.408
  Chirality :  0.045   0.304   1678
  Planarity :  0.007   0.127   1792
  Dihedral  :  7.084  50.702   1416
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 16.05
  Ramachandran Plot:
    Outliers :  1.15 %
    Allowed  :  7.82 %
    Favored  : 91.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.56 %
    Twisted Proline : 1.75 %
    Twisted General : 0.64 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.63 (0.24), residues: 1304
  helix:  1.43 (0.18), residues: 757
  sheet: -2.13 (0.44), residues: 115
  loop : -3.47 (0.27), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 157 
 TYR   0.026   0.002   TYR B 106 
 PHE   0.039   0.002   PHE A 210 
 TRP   0.027   0.001   TRP B 247 
 HIS   0.010   0.002   HIS C 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (10555)
  covalent geometry    : angle       0.78168 (14399)
  SS BOND              : bond        0.00448 (    5)
  SS BOND              : angle       4.40550 (   10)
  hydrogen bonds       : bond        0.04351 (  627)
  hydrogen bonds       : angle       5.01040 ( 1839)

*********************** 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
  185 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.402 
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  243 ASN cc_start: 0.9091 (t0) cc_final: 0.8794 (t0)
REVERT: A  290 ASN cc_start: 0.9019 (t0) cc_final: 0.8598 (p0)
REVERT: A  554 TYR cc_start: 0.8694 (t80) cc_final: 0.8183 (t80)
REVERT: B   93 MET cc_start: 0.9232 (mmt) cc_final: 0.8846 (mmm)
REVERT: B  172 LEU cc_start: 0.9472 (mm) cc_final: 0.9250 (mm)
REVERT: B  177 PHE cc_start: 0.9186 (m-80) cc_final: 0.8851 (m-80)
REVERT: B  233 MET cc_start: 0.8790 (ttt) cc_final: 0.8477 (ttt)
REVERT: B  385 ASP cc_start: 0.8309 (m-30) cc_final: 0.7199 (m-30)
REVERT: B  386 PHE cc_start: 0.9051 (t80) cc_final: 0.8457 (t80)
REVERT: B  388 PHE cc_start: 0.9470 (m-10) cc_final: 0.9204 (m-10)
REVERT: B  414 ILE cc_start: 0.9096 (mt) cc_final: 0.8752 (mt)
REVERT: C   40 PHE cc_start: 0.9573 (t80) cc_final: 0.9339 (t80)
REVERT: C   41 PHE cc_start: 0.9523 (m-80) cc_final: 0.9138 (m-10)
REVERT: C   90 TYR cc_start: 0.8880 (t80) cc_final: 0.8355 (t80)
REVERT: C   99 GLU cc_start: 0.8374 (pt0) cc_final: 0.8052 (pt0)
REVERT: C  138 LEU cc_start: 0.9445 (mt) cc_final: 0.9236 (mt)
REVERT: C  178 PHE cc_start: 0.9392 (t80) cc_final: 0.9160 (t80)
REVERT: C  224 MET cc_start: 0.9468 (mmp) cc_final: 0.9239 (mmm)
REVERT: D   23 PHE cc_start: 0.8401 (m-80) cc_final: 0.7976 (m-80)
REVERT: D   66 PHE cc_start: 0.9246 (t80) cc_final: 0.8981 (m-10)
REVERT: D   82 ARG cc_start: 0.8824 (ttp80) cc_final: 0.8598 (tpt90)
REVERT: D   95 THR cc_start: 0.8247 (m) cc_final: 0.7672 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 185
  average time/residue: 0.0802
  time to fit residues: 22.7562
Evaluate side-chains
  138 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 30 optimal weight:    9.9990
   chunk 32 optimal weight:    8.9990
   chunk 106 optimal weight:    7.9990
   chunk 50 optimal weight:    9.9990
   chunk 37 optimal weight:    0.6980
   chunk 80 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 111 optimal weight:    6.9990
   chunk 74 optimal weight:    0.0370
   chunk 26 optimal weight:    3.9990
   chunk 119 optimal weight:   10.0000
   overall best weight:    1.6862

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

Flipped N/Q/H residues before XYZ refinement:
A  74 HIS
A 305 GLN
A 531 ASN
A 573 ASN
A 612 ASN
B 222 GLN
B 405 ASN
** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 136 ASN
** D  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.050423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.043254 restraints weight = 74961.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.044354 restraints weight = 47933.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.045155 restraints weight = 33510.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.045673 restraints weight = 25976.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.046012 restraints weight = 21547.784|
|-----------------------------------------------------------------------------|
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.5306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  10560  Z= 0.158
  Angle     :  0.776  12.241  14409  Z= 0.398
  Chirality :  0.044   0.304   1678
  Planarity :  0.006   0.132   1792
  Dihedral  :  6.703  49.042   1416
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 16.25
  Ramachandran Plot:
    Outliers :  1.00 %
    Allowed  :  7.75 %
    Favored  : 91.26 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  3.36 %
    Favored  : 96.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.56 %
    Twisted Proline : 3.51 %
    Twisted General : 0.64 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.50 (0.24), residues: 1304
  helix:  1.41 (0.19), residues: 749
  sheet: -1.80 (0.45), residues: 121
  loop : -3.15 (0.28), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 342 
 TYR   0.023   0.002   TYR C 218 
 PHE   0.032   0.002   PHE A 327 
 TRP   0.024   0.001   TRP B 247 
 HIS   0.009   0.001   HIS C 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (10555)
  covalent geometry    : angle       0.76816 (14399)
  SS BOND              : bond        0.00796 (    5)
  SS BOND              : angle       4.29202 (   10)
  hydrogen bonds       : bond        0.04242 (  627)
  hydrogen bonds       : angle       4.98686 ( 1839)

*********************** 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
  188 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 187
  time to evaluate  : 0.413 
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  290 ASN cc_start: 0.9032 (t0) cc_final: 0.8589 (p0)
REVERT: B   93 MET cc_start: 0.9257 (mmt) cc_final: 0.8876 (mmm)
REVERT: B  172 LEU cc_start: 0.9485 (mm) cc_final: 0.9259 (mm)
REVERT: B  177 PHE cc_start: 0.9257 (m-80) cc_final: 0.8913 (m-80)
REVERT: B  181 TYR cc_start: 0.9316 (t80) cc_final: 0.9053 (t80)
REVERT: B  219 LEU cc_start: 0.9241 (pt) cc_final: 0.9003 (pp)
REVERT: B  233 MET cc_start: 0.8859 (ttt) cc_final: 0.8567 (ttt)
REVERT: B  385 ASP cc_start: 0.8266 (m-30) cc_final: 0.7243 (m-30)
REVERT: B  386 PHE cc_start: 0.8994 (t80) cc_final: 0.8426 (t80)
REVERT: B  388 PHE cc_start: 0.9420 (m-10) cc_final: 0.9177 (m-10)
REVERT: B  414 ILE cc_start: 0.9206 (mt) cc_final: 0.8858 (mt)
REVERT: B  437 ILE cc_start: 0.8953 (tp) cc_final: 0.8752 (tp)
REVERT: B  445 PHE cc_start: 0.9460 (m-80) cc_final: 0.9047 (m-80)
REVERT: B  466 TYR cc_start: 0.7377 (m-80) cc_final: 0.7104 (m-80)
REVERT: C   40 PHE cc_start: 0.9640 (t80) cc_final: 0.9297 (t80)
REVERT: C   41 PHE cc_start: 0.9513 (m-80) cc_final: 0.9134 (m-10)
REVERT: C   90 TYR cc_start: 0.8956 (t80) cc_final: 0.8558 (t80)
REVERT: C   99 GLU cc_start: 0.8331 (pt0) cc_final: 0.8037 (pt0)
REVERT: C  119 TYR cc_start: 0.8933 (t80) cc_final: 0.8503 (t80)
REVERT: C  132 PHE cc_start: 0.9217 (m-80) cc_final: 0.8814 (m-80)
REVERT: C  138 LEU cc_start: 0.9421 (mt) cc_final: 0.9201 (mt)
REVERT: C  140 ASP cc_start: 0.8819 (m-30) cc_final: 0.8619 (m-30)
REVERT: C  224 MET cc_start: 0.9485 (mmp) cc_final: 0.9240 (mmm)
REVERT: D   10 GLU cc_start: 0.9295 (tp30) cc_final: 0.9040 (tp30)
REVERT: D   23 PHE cc_start: 0.8477 (m-80) cc_final: 0.7986 (m-80)
REVERT: D   66 PHE cc_start: 0.9345 (t80) cc_final: 0.8955 (m-10)
REVERT: D   95 THR cc_start: 0.8145 (m) cc_final: 0.7508 (m)
  outliers start: 1
  outliers final: 0
  residues processed: 187
  average time/residue: 0.0888
  time to fit residues: 25.0455
Evaluate side-chains
  138 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 97 optimal weight:    9.9990
   chunk 35 optimal weight:    4.9990
   chunk 14 optimal weight:   10.0000
   chunk 50 optimal weight:   10.0000
   chunk 48 optimal weight:    0.9990
   chunk 51 optimal weight:    9.9990
   chunk 118 optimal weight:    7.9990
   chunk 103 optimal weight:   10.0000
   chunk 15 optimal weight:    5.9990
   chunk 81 optimal weight:    5.9990
   chunk 90 optimal weight:    3.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 237 GLN
A 305 GLN
A 573 ASN
** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  68 GLN
C 136 ASN
** C 171 HIS ** 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  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 = 0.3173 r_free = 0.3173 target = 0.049234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.042353 restraints weight = 79898.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.043479 restraints weight = 50960.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.044224 restraints weight = 35291.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.044703 restraints weight = 27247.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.044963 restraints weight = 22326.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.5599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071  10560  Z= 0.233
  Angle     :  0.805  13.055  14409  Z= 0.418
  Chirality :  0.044   0.311   1678
  Planarity :  0.006   0.114   1792
  Dihedral  :  6.775  47.562   1416
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 18.28
  Ramachandran Plot:
    Outliers :  0.92 %
    Allowed  :  8.74 %
    Favored  : 90.34 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  2.99 %
    Favored  : 96.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.56 %
    Twisted Proline : 3.51 %
    Twisted General : 0.40 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.71 (0.23), residues: 1304
  helix:  1.15 (0.18), residues: 752
  sheet: -1.83 (0.44), residues: 116
  loop : -3.08 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 342 
 TYR   0.025   0.002   TYR A 196 
 PHE   0.022   0.002   PHE B 465 
 TRP   0.026   0.002   TRP D  36 
 HIS   0.015   0.002   HIS C 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00494 (10555)
  covalent geometry    : angle       0.79666 (14399)
  SS BOND              : bond        0.00737 (    5)
  SS BOND              : angle       4.54807 (   10)
  hydrogen bonds       : bond        0.04239 (  627)
  hydrogen bonds       : angle       5.13920 ( 1839)

*********************** 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  : 0.410 
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: 0.9063 (t0) cc_final: 0.8413 (t0)
REVERT: A  343 MET cc_start: 0.9145 (tpt) cc_final: 0.8781 (tpt)
REVERT: B   93 MET cc_start: 0.9267 (mmt) cc_final: 0.8892 (mmm)
REVERT: B  106 TYR cc_start: 0.8871 (m-10) cc_final: 0.8230 (m-10)
REVERT: B  177 PHE cc_start: 0.9241 (m-80) cc_final: 0.8979 (m-80)
REVERT: B  184 GLU cc_start: 0.9170 (mp0) cc_final: 0.8635 (mp0)
REVERT: B  233 MET cc_start: 0.8849 (ttt) cc_final: 0.8575 (ttt)
REVERT: B  385 ASP cc_start: 0.8318 (m-30) cc_final: 0.7307 (m-30)
REVERT: B  386 PHE cc_start: 0.8990 (t80) cc_final: 0.8449 (t80)
REVERT: B  388 PHE cc_start: 0.9368 (m-10) cc_final: 0.8986 (m-10)
REVERT: B  410 CYS cc_start: 0.9766 (m) cc_final: 0.9564 (m)
REVERT: B  414 ILE cc_start: 0.9200 (mt) cc_final: 0.8887 (mt)
REVERT: B  445 PHE cc_start: 0.9444 (m-80) cc_final: 0.9120 (m-80)
REVERT: C   40 PHE cc_start: 0.9648 (t80) cc_final: 0.9327 (t80)
REVERT: C   41 PHE cc_start: 0.9506 (m-80) cc_final: 0.9098 (m-10)
REVERT: C   90 TYR cc_start: 0.8969 (t80) cc_final: 0.8515 (t80)
REVERT: C   99 GLU cc_start: 0.8345 (pt0) cc_final: 0.8072 (pt0)
REVERT: C  119 TYR cc_start: 0.8912 (t80) cc_final: 0.8457 (t80)
REVERT: C  218 TYR cc_start: 0.9535 (m-80) cc_final: 0.9134 (m-80)
REVERT: C  224 MET cc_start: 0.9494 (mmp) cc_final: 0.9277 (mmm)
REVERT: D   23 PHE cc_start: 0.8562 (m-80) cc_final: 0.8000 (m-80)
REVERT: D   66 PHE cc_start: 0.9251 (t80) cc_final: 0.9046 (m-10)
REVERT: D   95 THR cc_start: 0.8275 (m) cc_final: 0.7628 (m)
  outliers start: 2
  outliers final: 0
  residues processed: 173
  average time/residue: 0.0866
  time to fit residues: 22.6530
Evaluate side-chains
  136 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 100 optimal weight:   20.0000
   chunk 86 optimal weight:    0.8980
   chunk 20 optimal weight:    4.9990
   chunk 84 optimal weight:   20.0000
   chunk 53 optimal weight:    2.9990
   chunk 88 optimal weight:    5.9990
   chunk 30 optimal weight:    9.9990
   chunk 34 optimal weight:    9.9990
   chunk 115 optimal weight:    0.9990
   chunk 28 optimal weight:   10.0000
   chunk 38 optimal weight:    8.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 305 GLN
A 573 ASN
A 610 HIS
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 136 ASN ** 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  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 = 0.3180 r_free = 0.3180 target = 0.049641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.043103 restraints weight = 78698.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.044031 restraints weight = 51110.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.044775 restraints weight = 36396.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.045266 restraints weight = 28316.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.045566 restraints weight = 23339.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.5834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  10560  Z= 0.189
  Angle     :  0.790  17.508  14409  Z= 0.402
  Chirality :  0.044   0.332   1678
  Planarity :  0.007   0.160   1792
  Dihedral  :  6.513  46.675   1416
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 17.27
  Ramachandran Plot:
    Outliers :  0.92 %
    Allowed  :  8.21 %
    Favored  : 90.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.56 %
    Twisted Proline : 1.75 %
    Twisted General : 0.40 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.61 (0.23), residues: 1304
  helix:  1.21 (0.18), residues: 752
  sheet: -1.82 (0.44), residues: 115
  loop : -2.99 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 342 
 TYR   0.021   0.002   TYR A 196 
 PHE   0.025   0.002   PHE A 210 
 TRP   0.028   0.002   TRP C 174 
 HIS   0.012   0.002   HIS C 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 (10555)
  covalent geometry    : angle       0.77776 (14399)
  SS BOND              : bond        0.01077 (    5)
  SS BOND              : angle       5.29470 (   10)
  hydrogen bonds       : bond        0.04150 (  627)
  hydrogen bonds       : angle       5.04621 ( 1839)

*********************** 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
  173 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.394 
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: 0.9190 (t0) cc_final: 0.8563 (t0)
REVERT: A  631 LEU cc_start: 0.9271 (tt) cc_final: 0.9051 (pp)
REVERT: B   93 MET cc_start: 0.9258 (mmt) cc_final: 0.8900 (mmm)
REVERT: B  106 TYR cc_start: 0.8693 (m-10) cc_final: 0.8472 (m-10)
REVERT: B  177 PHE cc_start: 0.9258 (m-80) cc_final: 0.8979 (m-80)
REVERT: B  233 MET cc_start: 0.8854 (ttt) cc_final: 0.8561 (ttt)
REVERT: B  385 ASP cc_start: 0.8233 (m-30) cc_final: 0.7020 (m-30)
REVERT: B  386 PHE cc_start: 0.8945 (t80) cc_final: 0.8409 (t80)
REVERT: B  388 PHE cc_start: 0.9304 (m-10) cc_final: 0.8832 (m-10)
REVERT: B  410 CYS cc_start: 0.9760 (m) cc_final: 0.9486 (m)
REVERT: B  414 ILE cc_start: 0.9157 (mt) cc_final: 0.8837 (mt)
REVERT: B  445 PHE cc_start: 0.9377 (m-80) cc_final: 0.9014 (m-80)
REVERT: B  466 TYR cc_start: 0.7488 (m-80) cc_final: 0.7193 (m-80)
REVERT: C   35 LEU cc_start: 0.9582 (tt) cc_final: 0.9344 (mm)
REVERT: C   40 PHE cc_start: 0.9604 (t80) cc_final: 0.9331 (t80)
REVERT: C   41 PHE cc_start: 0.9462 (m-80) cc_final: 0.9034 (m-10)
REVERT: C   42 TRP cc_start: 0.9374 (t60) cc_final: 0.8903 (t60)
REVERT: C   90 TYR cc_start: 0.8881 (t80) cc_final: 0.8435 (t80)
REVERT: C  119 TYR cc_start: 0.8935 (t80) cc_final: 0.8513 (t80)
REVERT: C  218 TYR cc_start: 0.9581 (m-80) cc_final: 0.9064 (m-80)
REVERT: C  224 MET cc_start: 0.9504 (mmp) cc_final: 0.9236 (mmm)
REVERT: D   10 GLU cc_start: 0.9274 (tp30) cc_final: 0.9024 (tp30)
REVERT: D   23 PHE cc_start: 0.8522 (m-80) cc_final: 0.8012 (m-80)
REVERT: D   95 THR cc_start: 0.8105 (m) cc_final: 0.7359 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.0796
  time to fit residues: 20.6911
Evaluate side-chains
  129 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 76 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 13 optimal weight:    9.9990
   chunk 127 optimal weight:    2.9990
   chunk 36 optimal weight:    9.9990
   chunk 5 optimal weight:    6.9990
   chunk 92 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0570
   chunk 60 optimal weight:    6.9990
   chunk 105 optimal weight:    5.9990
   overall best weight:    2.0106

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

Flipped N/Q/H residues before XYZ refinement:
A 573 ASN
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 171 HIS
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.050215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.043257 restraints weight = 77088.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.044398 restraints weight = 49790.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.045171 restraints weight = 34496.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.045674 restraints weight = 26642.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.046076 restraints weight = 21931.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.6138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075  10560  Z= 0.169
  Angle     :  0.788  17.229  14409  Z= 0.406
  Chirality :  0.044   0.300   1678
  Planarity :  0.006   0.142   1792
  Dihedral  :  6.344  44.978   1416
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 16.98
  Ramachandran Plot:
    Outliers :  1.00 %
    Allowed  :  7.90 %
    Favored  : 91.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.56 %
    Twisted Proline : 1.75 %
    Twisted General : 0.40 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.67 (0.23), residues: 1304
  helix:  1.11 (0.18), residues: 749
  sheet: -1.69 (0.45), residues: 117
  loop : -2.92 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 342 
 TYR   0.023   0.002   TYR A 196 
 PHE   0.025   0.002   PHE A 677 
 TRP   0.028   0.002   TRP D  85 
 HIS   0.008   0.001   HIS C 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (10555)
  covalent geometry    : angle       0.77173 (14399)
  SS BOND              : bond        0.00823 (    5)
  SS BOND              : angle       6.04619 (   10)
  hydrogen bonds       : bond        0.04181 (  627)
  hydrogen bonds       : angle       5.07385 ( 1839)

*********************** 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
  179 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  290 ASN cc_start: 0.9202 (t0) cc_final: 0.8648 (t0)
REVERT: A  631 LEU cc_start: 0.9284 (tt) cc_final: 0.9062 (pp)
REVERT: B   93 MET cc_start: 0.9301 (mmt) cc_final: 0.9029 (mmp)
REVERT: B  172 LEU cc_start: 0.9505 (mm) cc_final: 0.9296 (mm)
REVERT: B  177 PHE cc_start: 0.9316 (m-80) cc_final: 0.9035 (m-80)
REVERT: B  233 MET cc_start: 0.8865 (ttt) cc_final: 0.8581 (ttt)
REVERT: B  385 ASP cc_start: 0.8209 (m-30) cc_final: 0.7020 (m-30)
REVERT: B  386 PHE cc_start: 0.8983 (t80) cc_final: 0.8376 (t80)
REVERT: B  388 PHE cc_start: 0.9285 (m-10) cc_final: 0.8860 (m-10)
REVERT: B  418 LEU cc_start: 0.9811 (tt) cc_final: 0.9551 (mt)
REVERT: B  422 LEU cc_start: 0.9632 (mt) cc_final: 0.9401 (pp)
REVERT: B  445 PHE cc_start: 0.9432 (m-80) cc_final: 0.9059 (m-80)
REVERT: B  466 TYR cc_start: 0.7451 (m-80) cc_final: 0.7008 (m-80)
REVERT: C   35 LEU cc_start: 0.9588 (tt) cc_final: 0.9359 (mm)
REVERT: C   40 PHE cc_start: 0.9593 (t80) cc_final: 0.9307 (t80)
REVERT: C   41 PHE cc_start: 0.9502 (m-80) cc_final: 0.9034 (m-10)
REVERT: C   42 TRP cc_start: 0.9524 (t60) cc_final: 0.9173 (t60)
REVERT: C   90 TYR cc_start: 0.8891 (t80) cc_final: 0.8369 (t80)
REVERT: C  119 TYR cc_start: 0.8924 (t80) cc_final: 0.8492 (t80)
REVERT: C  218 TYR cc_start: 0.9559 (m-80) cc_final: 0.9125 (m-80)
REVERT: C  224 MET cc_start: 0.9473 (mmp) cc_final: 0.9211 (mmm)
REVERT: D   10 GLU cc_start: 0.9399 (tp30) cc_final: 0.9166 (tp30)
REVERT: D   14 LEU cc_start: 0.9625 (mm) cc_final: 0.9138 (mm)
REVERT: D   23 PHE cc_start: 0.8534 (m-80) cc_final: 0.8070 (m-80)
REVERT: D   56 TYR cc_start: 0.9034 (m-80) cc_final: 0.8789 (m-80)
REVERT: D   95 THR cc_start: 0.8094 (m) cc_final: 0.7625 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 179
  average time/residue: 0.0700
  time to fit residues: 19.7081
Evaluate side-chains
  130 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 41 optimal weight:   10.0000
   chunk 29 optimal weight:    0.0020
   chunk 51 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 62 optimal weight:    5.9990
   chunk 105 optimal weight:    8.9990
   chunk 113 optimal weight:    5.9990
   chunk 129 optimal weight:   30.0000
   chunk 42 optimal weight:    8.9990
   overall best weight:    3.5996

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

Flipped N/Q/H residues before XYZ refinement:
A 562 ASN
A 573 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  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.049017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.042458 restraints weight = 79226.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.043394 restraints weight = 51434.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.044103 restraints weight = 37404.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.044598 restraints weight = 29052.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.044876 restraints weight = 23927.743|
|-----------------------------------------------------------------------------|
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.6279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068  10560  Z= 0.208
  Angle     :  0.792  13.856  14409  Z= 0.411
  Chirality :  0.044   0.283   1678
  Planarity :  0.007   0.133   1792
  Dihedral  :  6.319  45.454   1416
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 18.53
  Ramachandran Plot:
    Outliers :  0.92 %
    Allowed  :  8.59 %
    Favored  : 90.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.56 %
    Twisted Proline : 1.75 %
    Twisted General : 0.32 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.76 (0.23), residues: 1304
  helix:  1.04 (0.18), residues: 754
  sheet: -1.78 (0.43), residues: 118
  loop : -3.01 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 342 
 TYR   0.021   0.002   TYR A 196 
 PHE   0.036   0.002   PHE C 205 
 TRP   0.025   0.002   TRP B 247 
 HIS   0.009   0.002   HIS C  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 (10555)
  covalent geometry    : angle       0.78175 (14399)
  SS BOND              : bond        0.00872 (    5)
  SS BOND              : angle       4.96499 (   10)
  hydrogen bonds       : bond        0.04159 (  627)
  hydrogen bonds       : angle       5.23001 ( 1839)

*********************** 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
  175 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.457 
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: 0.9180 (tttm) cc_final: 0.8758 (tmtt)
REVERT: A  215 MET cc_start: 0.9006 (mmm) cc_final: 0.8610 (mmm)
REVERT: A  290 ASN cc_start: 0.9191 (t0) cc_final: 0.8732 (t0)
REVERT: B   93 MET cc_start: 0.9308 (mmt) cc_final: 0.9031 (mmp)
REVERT: B  106 TYR cc_start: 0.8770 (m-10) cc_final: 0.8179 (m-10)
REVERT: B  168 ILE cc_start: 0.9290 (mm) cc_final: 0.9084 (pt)
REVERT: B  177 PHE cc_start: 0.9315 (m-80) cc_final: 0.9038 (m-80)
REVERT: B  184 GLU cc_start: 0.9297 (mp0) cc_final: 0.8603 (mp0)
REVERT: B  233 MET cc_start: 0.8825 (ttt) cc_final: 0.8578 (ttt)
REVERT: B  385 ASP cc_start: 0.8254 (m-30) cc_final: 0.7257 (m-30)
REVERT: B  386 PHE cc_start: 0.8959 (t80) cc_final: 0.8479 (t80)
REVERT: B  388 PHE cc_start: 0.9320 (m-10) cc_final: 0.8927 (m-10)
REVERT: B  418 LEU cc_start: 0.9829 (tt) cc_final: 0.9581 (mt)
REVERT: B  422 LEU cc_start: 0.9636 (mt) cc_final: 0.9412 (pp)
REVERT: B  445 PHE cc_start: 0.9443 (m-80) cc_final: 0.9040 (m-80)
REVERT: C   35 LEU cc_start: 0.9602 (tt) cc_final: 0.9368 (mm)
REVERT: C   40 PHE cc_start: 0.9619 (t80) cc_final: 0.9311 (t80)
REVERT: C   41 PHE cc_start: 0.9494 (m-80) cc_final: 0.9042 (m-10)
REVERT: C   90 TYR cc_start: 0.8908 (t80) cc_final: 0.8333 (t80)
REVERT: C  119 TYR cc_start: 0.8926 (t80) cc_final: 0.8484 (t80)
REVERT: C  224 MET cc_start: 0.9492 (mmp) cc_final: 0.9215 (mmm)
REVERT: D   10 GLU cc_start: 0.9341 (tp30) cc_final: 0.9019 (tp30)
REVERT: D   14 LEU cc_start: 0.9715 (mm) cc_final: 0.9102 (mm)
REVERT: D   23 PHE cc_start: 0.8477 (m-80) cc_final: 0.8012 (m-80)
REVERT: D   56 TYR cc_start: 0.8912 (m-80) cc_final: 0.8658 (m-80)
REVERT: D   95 THR cc_start: 0.8122 (m) cc_final: 0.7347 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 175
  average time/residue: 0.0709
  time to fit residues: 19.3316
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  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 15 optimal weight:    9.9990
   chunk 29 optimal weight:    5.9990
   chunk 47 optimal weight:   20.0000
   chunk 57 optimal weight:    9.9990
   chunk 70 optimal weight:    0.8980
   chunk 56 optimal weight:    3.9990
   chunk 117 optimal weight:   20.0000
   chunk 30 optimal weight:    5.9990
   chunk 91 optimal weight:    0.0050
   chunk 71 optimal weight:    5.9990
   chunk 55 optimal weight:    0.5980
   overall best weight:    2.2998

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

Flipped N/Q/H residues before XYZ refinement:
A 454 GLN
A 573 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  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.049980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.043096 restraints weight = 76847.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.044205 restraints weight = 49800.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.044970 restraints weight = 34455.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.045519 restraints weight = 26539.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.045835 restraints weight = 21527.553|
|-----------------------------------------------------------------------------|
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.6425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067  10560  Z= 0.169
  Angle     :  0.803  16.374  14409  Z= 0.411
  Chirality :  0.044   0.282   1678
  Planarity :  0.006   0.128   1792
  Dihedral  :  6.210  44.536   1416
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 17.65
  Ramachandran Plot:
    Outliers :  0.84 %
    Allowed  :  8.21 %
    Favored  : 90.95 %
  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 : 0.32 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.64 (0.24), residues: 1304
  helix:  1.09 (0.18), residues: 761
  sheet: -1.76 (0.44), residues: 118
  loop : -2.92 (0.30), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 342 
 TYR   0.032   0.002   TYR C 119 
 PHE   0.032   0.002   PHE A 181 
 TRP   0.024   0.002   TRP B 247 
 HIS   0.007   0.001   HIS C  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 (10555)
  covalent geometry    : angle       0.78858 (14399)
  SS BOND              : bond        0.00619 (    5)
  SS BOND              : angle       5.74564 (   10)
  hydrogen bonds       : bond        0.04040 (  627)
  hydrogen bonds       : angle       5.19430 ( 1839)

********************** 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  : 0.489 
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  195 CYS cc_start: 0.7739 (m) cc_final: 0.7484 (m)
REVERT: A  290 ASN cc_start: 0.9199 (t0) cc_final: 0.8706 (t0)
REVERT: B   93 MET cc_start: 0.9281 (mmt) cc_final: 0.8960 (mmp)
REVERT: B  106 TYR cc_start: 0.8654 (m-10) cc_final: 0.8071 (m-10)
REVERT: B  177 PHE cc_start: 0.9346 (m-80) cc_final: 0.9092 (m-80)
REVERT: B  184 GLU cc_start: 0.9296 (mp0) cc_final: 0.8552 (mp0)
REVERT: B  219 LEU cc_start: 0.9231 (pt) cc_final: 0.9003 (pp)
REVERT: B  233 MET cc_start: 0.8879 (ttt) cc_final: 0.8591 (ttt)
REVERT: B  385 ASP cc_start: 0.8160 (m-30) cc_final: 0.7851 (p0)
REVERT: B  386 PHE cc_start: 0.9018 (t80) cc_final: 0.8603 (t80)
REVERT: B  388 PHE cc_start: 0.9286 (m-10) cc_final: 0.9002 (m-10)
REVERT: B  414 ILE cc_start: 0.9171 (mt) cc_final: 0.8886 (mt)
REVERT: B  422 LEU cc_start: 0.9640 (mt) cc_final: 0.9355 (pp)
REVERT: B  445 PHE cc_start: 0.9442 (m-80) cc_final: 0.9047 (m-80)
REVERT: B  457 MET cc_start: 0.9250 (ptt) cc_final: 0.8995 (tmm)
REVERT: B  466 TYR cc_start: 0.7198 (m-80) cc_final: 0.6651 (m-80)
REVERT: C   35 LEU cc_start: 0.9601 (tt) cc_final: 0.9368 (mm)
REVERT: C   40 PHE cc_start: 0.9606 (t80) cc_final: 0.9329 (t80)
REVERT: C   41 PHE cc_start: 0.9460 (m-80) cc_final: 0.9088 (m-10)
REVERT: C   90 TYR cc_start: 0.8845 (t80) cc_final: 0.8304 (t80)
REVERT: C  211 GLU cc_start: 0.6884 (tm-30) cc_final: 0.6562 (tm-30)
REVERT: C  224 MET cc_start: 0.9495 (mmp) cc_final: 0.9229 (mmm)
REVERT: D   23 PHE cc_start: 0.8481 (m-80) cc_final: 0.8032 (m-80)
REVERT: D   56 TYR cc_start: 0.8982 (m-80) cc_final: 0.8724 (m-80)
REVERT: D   95 THR cc_start: 0.8105 (m) cc_final: 0.7290 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 175
  average time/residue: 0.0753
  time to fit residues: 20.5075
Evaluate side-chains
  133 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 93 optimal weight:    0.9990
   chunk 126 optimal weight:   10.0000
   chunk 87 optimal weight:    0.9990
   chunk 46 optimal weight:   10.0000
   chunk 50 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 103 optimal weight:    9.9990
   chunk 117 optimal weight:   20.0000
   chunk 101 optimal weight:   10.0000
   chunk 38 optimal weight:    0.0980
   chunk 57 optimal weight:    9.9990
   overall best weight:    0.7986

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

Flipped N/Q/H residues before XYZ refinement:
A 573 ASN
** B 204 ASN ** 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   8 ASN
** D  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.051274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.043968 restraints weight = 74786.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.045114 restraints weight = 47290.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.045992 restraints weight = 32569.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.046613 restraints weight = 25279.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.047023 restraints weight = 20298.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.6627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070  10560  Z= 0.149
  Angle     :  0.801  14.907  14409  Z= 0.410
  Chirality :  0.044   0.279   1678
  Planarity :  0.006   0.124   1792
  Dihedral  :  6.074  43.626   1416
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 15.67
  Ramachandran Plot:
    Outliers :  0.84 %
    Allowed  :  8.13 %
    Favored  : 91.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.56 %
    Twisted Proline : 1.75 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.60 (0.24), residues: 1304
  helix:  1.13 (0.18), residues: 755
  sheet: -1.75 (0.44), residues: 120
  loop : -2.85 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 342 
 TYR   0.022   0.002   TYR C 119 
 PHE   0.054   0.002   PHE A 682 
 TRP   0.019   0.002   TRP C 174 
 HIS   0.013   0.001   HIS C 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (10555)
  covalent geometry    : angle       0.78928 (14399)
  SS BOND              : bond        0.00693 (    5)
  SS BOND              : angle       5.23188 (   10)
  hydrogen bonds       : bond        0.04033 (  627)
  hydrogen bonds       : angle       5.14069 ( 1839)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1566.98 seconds
wall clock time: 28 minutes 2.37 seconds (1682.37 seconds total)