Starting phenix.real_space_refine
on Fri Feb 14 15:16:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5fn3_3238/02_2025/5fn3_3238.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5fn3_3238/02_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_3238/02_2025/5fn3_3238.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5fn3_3238/02_2025/5fn3_3238.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5fn3_3238/02_2025/5fn3_3238.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5fn3_3238/02_2025/5fn3_3238.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      39      5.16       5
     C    6738      2.51       5
     N    1679      2.21       5
     O    1835      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10291
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 5222
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 665, 5222
          Classifications: {'peptide': 665}
          Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 627}
    Chain: "B"
      Number of atoms: 2234
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2234
          Classifications: {'peptide': 286}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'CIS': 7, 'PTRANS': 8, 'TRANS': 270}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "C"
      Number of atoms: 1868
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 243, 1868
          Classifications: {'peptide': 243}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 235}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "D"
      Number of atoms: 847
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 847
          Classifications: {'peptide': 100}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 94}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "G"
      Number of atoms: 120
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 120
          Classifications: {'peptide': 24}
          Link IDs: {'TRANS': 23}
  Time building chain proxies: 5.49, per 1000 atoms: 0.53
  Number of scatterers: 10291
  At special positions: 0
  Unit cell: (92.4, 144.2, 110.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      39     16.00
     O    1835      8.00
     N    1679      7.00
     C    6738      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  50 " - pdb=" SG  CYS A  62 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A 140 " - pdb=" SG  CYS A 159 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 195 " - pdb=" SG  CYS A 213 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 230 " - pdb=" SG  CYS A 248 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 586 " - pdb=" SG  CYS A 620 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.73
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 5 sheets defined
      60.4% alpha, 5.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.98
  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: 2.92

  Time building geometry restraints manager: 3.11 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:             0.260
  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:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     24.060
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.520
-------------------------------------------------------------------------------
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  10555  Z= 0.729
  Angle     :  1.812  15.892  14399  Z= 1.274
  Chirality :  0.102   0.602   1678
  Planarity :  0.009   0.126   1792
  Dihedral  : 18.644 117.206   3664
  Min Nonbonded Distance : 1.021

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

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.54 (0.21), residues: 1304
  helix:  1.17 (0.16), residues: 733
  sheet: -3.06 (0.39), residues: 108
  loop : -4.37 (0.22), residues: 463

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

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

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

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

  2608 Ramachandran restraints generated.
    1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  389 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 125
    poor density    : 264
  time to evaluate  : 1.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 CYS cc_start: 0.8638 (OUTLIER) cc_final: 0.7372 (p)
REVERT: A   95 MET cc_start: 0.9366 (mmt) cc_final: 0.8684 (mmm)
REVERT: A  312 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9122 (pp)
REVERT: A  326 MET cc_start: 0.9223 (tpt) cc_final: 0.8945 (tmm)
REVERT: A  331 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8265 (tp40)
REVERT: A  333 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8192 (mp0)
REVERT: A  443 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7375 (t0)
REVERT: A  554 TYR cc_start: 0.9302 (t80) cc_final: 0.8785 (t80)
REVERT: A  574 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8331 (mt)
REVERT: A  654 LYS cc_start: 0.9010 (pttp) cc_final: 0.8778 (ptpp)
REVERT: A  655 ASP cc_start: 0.9191 (m-30) cc_final: 0.8822 (t0)
REVERT: B   93 MET cc_start: 0.8994 (mmm) cc_final: 0.8753 (mmm)
REVERT: B  117 PRO cc_start: 0.7582 (OUTLIER) cc_final: 0.7116 (Cg_endo)
REVERT: B  184 GLU cc_start: 0.9202 (OUTLIER) cc_final: 0.8946 (mm-30)
REVERT: B  385 ASP cc_start: 0.8333 (m-30) cc_final: 0.8052 (m-30)
REVERT: B  386 PHE cc_start: 0.9085 (t80) cc_final: 0.8459 (t80)
REVERT: B  401 SER cc_start: 0.8378 (t) cc_final: 0.8125 (p)
REVERT: C   24 THR cc_start: 0.9451 (m) cc_final: 0.9240 (p)
REVERT: C  152 ASP cc_start: 0.8709 (OUTLIER) cc_final: 0.8267 (p0)
REVERT: C  178 PHE cc_start: 0.9538 (t80) cc_final: 0.9267 (t80)
REVERT: D   23 PHE cc_start: 0.8725 (m-80) cc_final: 0.8167 (m-80)
REVERT: D   39 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.7302 (tpt170)
REVERT: D   49 GLU cc_start: 0.9465 (mm-30) cc_final: 0.9056 (pt0)
REVERT: D   66 PHE cc_start: 0.9400 (t80) cc_final: 0.9174 (m-10)
REVERT: D   95 THR cc_start: 0.6596 (m) cc_final: 0.6372 (p)
  outliers start: 125
  outliers final: 30
  residues processed: 341
  average time/residue: 0.2127
  time to fit residues: 105.0958
Evaluate side-chains
  204 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 164
  time to evaluate  : 1.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 109 optimal weight:    3.9990
   chunk 98 optimal weight:    0.8980
   chunk 54 optimal weight:   10.0000
   chunk 33 optimal weight:   10.0000
   chunk 66 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 101 optimal weight:    5.9990
   chunk 39 optimal weight:    6.9990
   chunk 61 optimal weight:    4.9990
   chunk 75 optimal weight:    6.9990
   chunk 118 optimal weight:    7.9990
   overall best weight:    2.7786

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

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

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.051119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.043862 restraints weight = 73680.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.044908 restraints weight = 48207.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.045665 restraints weight = 33879.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.3763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  10555  Z= 0.319
  Angle     :  0.930  12.606  14399  Z= 0.486
  Chirality :  0.050   0.319   1678
  Planarity :  0.008   0.136   1792
  Dihedral  :  8.230  64.512   1416
  Min Nonbonded Distance : 2.404

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

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.24), residues: 1304
  helix:  1.75 (0.19), residues: 764
  sheet: -2.50 (0.42), residues: 124
  loop : -4.05 (0.25), residues: 416

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

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

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

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

  2608 Ramachandran restraints generated.
    1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 220
  time to evaluate  : 1.225 
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: 0.9092 (t0) cc_final: 0.8599 (p0)
REVERT: A  554 TYR cc_start: 0.8668 (t80) cc_final: 0.8134 (t80)
REVERT: B  181 TYR cc_start: 0.9332 (t80) cc_final: 0.9062 (t80)
REVERT: B  233 MET cc_start: 0.8758 (ttt) cc_final: 0.8380 (ttt)
REVERT: B  385 ASP cc_start: 0.8547 (m-30) cc_final: 0.7476 (m-30)
REVERT: B  386 PHE cc_start: 0.9111 (t80) cc_final: 0.8622 (t80)
REVERT: B  388 PHE cc_start: 0.9603 (m-10) cc_final: 0.9340 (m-10)
REVERT: B  454 GLN cc_start: 0.9322 (tm-30) cc_final: 0.8880 (tm-30)
REVERT: C   41 PHE cc_start: 0.9440 (m-80) cc_final: 0.9206 (m-10)
REVERT: C   90 TYR cc_start: 0.8646 (t80) cc_final: 0.8030 (t80)
REVERT: C  132 PHE cc_start: 0.9614 (m-80) cc_final: 0.9359 (m-80)
REVERT: C  138 LEU cc_start: 0.9578 (mt) cc_final: 0.9346 (mt)
REVERT: C  152 ASP cc_start: 0.8826 (m-30) cc_final: 0.8541 (m-30)
REVERT: C  199 LEU cc_start: 0.9250 (mt) cc_final: 0.9044 (mt)
REVERT: C  204 THR cc_start: 0.9007 (p) cc_final: 0.8676 (p)
REVERT: C  218 TYR cc_start: 0.9261 (m-80) cc_final: 0.9017 (m-80)
REVERT: C  224 MET cc_start: 0.9445 (mmp) cc_final: 0.9231 (mmm)
REVERT: D   23 PHE cc_start: 0.8347 (m-80) cc_final: 0.8062 (m-80)
REVERT: D   25 PHE cc_start: 0.9231 (m-80) cc_final: 0.8961 (m-80)
REVERT: D   66 PHE cc_start: 0.9284 (t80) cc_final: 0.9019 (m-10)
  outliers start: 7
  outliers final: 0
  residues processed: 225
  average time/residue: 0.1856
  time to fit residues: 62.9302
Evaluate side-chains
  143 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 1.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 47 optimal weight:    0.0670
   chunk 93 optimal weight:    1.9990
   chunk 36 optimal weight:   10.0000
   chunk 13 optimal weight:    3.9990
   chunk 21 optimal weight:    8.9990
   chunk 39 optimal weight:    5.9990
   chunk 75 optimal weight:    4.9990
   chunk 90 optimal weight:    6.9990
   chunk 1 optimal weight:   10.0000
   chunk 71 optimal weight:   20.0000
   chunk 104 optimal weight:   10.0000
   overall best weight:    3.4126

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

Flipped N/Q/H residues before XYZ refinement:
A  55 ASN
A 194 GLN
A 197 GLN
** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 305 GLN
A 478 ASN
A 516 GLN
A 573 ASN
** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   8 ASN ** 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 = 0.3176 r_free = 0.3176 target = 0.050541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.043469 restraints weight = 77913.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.044511 restraints weight = 51620.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.045205 restraints weight = 36408.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.4478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  10555  Z= 0.300
  Angle     :  0.839  13.831  14399  Z= 0.437
  Chirality :  0.046   0.301   1678
  Planarity :  0.007   0.150   1792
  Dihedral  :  7.431  54.306   1416
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 17.56
  Ramachandran Plot:
    Outliers :  1.15 %
    Allowed  :  8.90 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  3.54 %
    Favored  : 96.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.56 %
    Twisted Proline : 3.51 %
    Twisted General : 0.80 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.24), residues: 1304
  helix:  1.60 (0.19), residues: 753
  sheet: -2.25 (0.43), residues: 120
  loop : -3.64 (0.26), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP B 247 
 HIS   0.010   0.002   HIS C  58 
 PHE   0.034   0.003   PHE A 302 
 TYR   0.030   0.002   TYR B 115 
 ARG   0.003   0.000   ARG A 520 

*********************** 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
  190 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 188
  time to evaluate  : 1.203 
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: 0.9061 (t0) cc_final: 0.8565 (p0)
REVERT: A  343 MET cc_start: 0.9329 (tpt) cc_final: 0.9127 (tpp)
REVERT: A  554 TYR cc_start: 0.8572 (t80) cc_final: 0.8212 (t80)
REVERT: B   93 MET cc_start: 0.9163 (mmm) cc_final: 0.8939 (mmm)
REVERT: B  182 LEU cc_start: 0.9903 (tp) cc_final: 0.9530 (pp)
REVERT: B  233 MET cc_start: 0.8701 (ttt) cc_final: 0.8327 (ttt)
REVERT: B  385 ASP cc_start: 0.8483 (m-30) cc_final: 0.7358 (m-30)
REVERT: B  386 PHE cc_start: 0.9029 (t80) cc_final: 0.8462 (t80)
REVERT: B  388 PHE cc_start: 0.9568 (m-10) cc_final: 0.9252 (m-10)
REVERT: B  408 ILE cc_start: 0.9653 (tp) cc_final: 0.9409 (pt)
REVERT: C   40 PHE cc_start: 0.9632 (t80) cc_final: 0.9310 (t80)
REVERT: C   41 PHE cc_start: 0.9529 (m-80) cc_final: 0.9154 (m-10)
REVERT: C   43 LEU cc_start: 0.9663 (mt) cc_final: 0.9444 (mt)
REVERT: C   90 TYR cc_start: 0.8971 (t80) cc_final: 0.8465 (t80)
REVERT: C   99 GLU cc_start: 0.8309 (pt0) cc_final: 0.8060 (pt0)
REVERT: C  218 TYR cc_start: 0.9380 (m-80) cc_final: 0.9067 (m-10)
REVERT: C  224 MET cc_start: 0.9460 (mmp) cc_final: 0.9172 (mmm)
REVERT: D   23 PHE cc_start: 0.8334 (m-80) cc_final: 0.7961 (m-80)
REVERT: D   62 VAL cc_start: 0.9617 (t) cc_final: 0.9174 (p)
REVERT: D   66 PHE cc_start: 0.9284 (t80) cc_final: 0.9036 (m-10)
REVERT: D   82 ARG cc_start: 0.8732 (ttp80) cc_final: 0.8465 (tpt90)
REVERT: D   95 THR cc_start: 0.8184 (m) cc_final: 0.7707 (m)
  outliers start: 2
  outliers final: 1
  residues processed: 189
  average time/residue: 0.2196
  time to fit residues: 61.9669
Evaluate side-chains
  133 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 132
  time to evaluate  : 1.250 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 119 optimal weight:    8.9990
   chunk 34 optimal weight:    4.9990
   chunk 98 optimal weight:    0.9990
   chunk 81 optimal weight:   10.0000
   chunk 75 optimal weight:    1.9990
   chunk 101 optimal weight:    9.9990
   chunk 76 optimal weight:    0.9990
   chunk 41 optimal weight:   10.0000
   chunk 44 optimal weight:    4.9990
   chunk 15 optimal weight:    6.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 237 GLN
A 606 GLN
** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   8 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 = 0.3194 r_free = 0.3194 target = 0.050496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.043291 restraints weight = 74588.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.044334 restraints weight = 48886.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.045170 restraints weight = 34130.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.4942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10555  Z= 0.238
  Angle     :  0.791  13.135  14399  Z= 0.408
  Chirality :  0.045   0.288   1678
  Planarity :  0.007   0.129   1792
  Dihedral  :  7.046  50.819   1416
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 16.68
  Ramachandran Plot:
    Outliers :  1.07 %
    Allowed  :  8.05 %
    Favored  : 90.87 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  3.18 %
    Favored  : 96.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.56 %
    Twisted Proline : 1.75 %
    Twisted General : 0.72 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.24), residues: 1304
  helix:  1.49 (0.19), residues: 754
  sheet: -2.11 (0.44), residues: 118
  loop : -3.38 (0.27), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP B 247 
 HIS   0.010   0.001   HIS C 197 
 PHE   0.048   0.002   PHE A 210 
 TYR   0.029   0.002   TYR D  18 
 ARG   0.004   0.000   ARG B 157 

*********************** 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
  186 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 185
  time to evaluate  : 1.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  290 ASN cc_start: 0.9005 (t0) cc_final: 0.8596 (p0)
REVERT: A  325 VAL cc_start: 0.9479 (t) cc_final: 0.9199 (t)
REVERT: A  554 TYR cc_start: 0.8721 (t80) cc_final: 0.8173 (t80)
REVERT: B   93 MET cc_start: 0.9257 (mmt) cc_final: 0.8867 (mmm)
REVERT: B  172 LEU cc_start: 0.9520 (mm) cc_final: 0.9306 (mm)
REVERT: B  233 MET cc_start: 0.8719 (ttt) cc_final: 0.8450 (ttt)
REVERT: B  385 ASP cc_start: 0.8361 (m-30) cc_final: 0.7277 (m-30)
REVERT: B  386 PHE cc_start: 0.9121 (t80) cc_final: 0.8496 (t80)
REVERT: B  388 PHE cc_start: 0.9500 (m-10) cc_final: 0.9232 (m-10)
REVERT: B  437 ILE cc_start: 0.8945 (tp) cc_final: 0.8732 (tp)
REVERT: B  445 PHE cc_start: 0.9552 (m-80) cc_final: 0.9212 (m-80)
REVERT: C   40 PHE cc_start: 0.9620 (t80) cc_final: 0.9293 (t80)
REVERT: C   41 PHE cc_start: 0.9508 (m-80) cc_final: 0.9133 (m-10)
REVERT: C   90 TYR cc_start: 0.8980 (t80) cc_final: 0.8420 (t80)
REVERT: C   99 GLU cc_start: 0.8341 (pt0) cc_final: 0.8026 (pt0)
REVERT: C  138 LEU cc_start: 0.9463 (mt) cc_final: 0.9241 (mt)
REVERT: C  224 MET cc_start: 0.9469 (mmp) cc_final: 0.9190 (mmm)
REVERT: D   23 PHE cc_start: 0.8446 (m-80) cc_final: 0.8068 (m-80)
REVERT: D   66 PHE cc_start: 0.9275 (t80) cc_final: 0.8957 (m-10)
REVERT: D   82 ARG cc_start: 0.8931 (ttp80) cc_final: 0.8693 (tpt90)
REVERT: D   95 THR cc_start: 0.8212 (m) cc_final: 0.7678 (m)
  outliers start: 1
  outliers final: 0
  residues processed: 186
  average time/residue: 0.1840
  time to fit residues: 52.3435
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  : 1.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 82 optimal weight:   10.0000
   chunk 7 optimal weight:    0.7980
   chunk 29 optimal weight:   10.0000
   chunk 75 optimal weight:    0.4980
   chunk 9 optimal weight:    0.9990
   chunk 124 optimal weight:    4.9990
   chunk 45 optimal weight:    9.9990
   chunk 104 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 84 optimal weight:    7.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
A 305 GLN
** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D   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 = 0.3208 r_free = 0.3208 target = 0.051199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.043862 restraints weight = 77222.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.044960 restraints weight = 49183.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.045761 restraints weight = 33874.017|
|-----------------------------------------------------------------------------|
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.5312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067  10555  Z= 0.222
  Angle     :  0.779  15.575  14399  Z= 0.397
  Chirality :  0.044   0.327   1678
  Planarity :  0.007   0.154   1792
  Dihedral  :  6.759  48.866   1416
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 15.71
  Ramachandran Plot:
    Outliers :  1.00 %
    Allowed  :  7.90 %
    Favored  : 91.10 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  2.90 %
    Favored  : 96.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.56 %
    Twisted Proline : 3.51 %
    Twisted General : 0.56 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.53 (0.24), residues: 1304
  helix:  1.36 (0.18), residues: 754
  sheet: -1.81 (0.46), residues: 121
  loop : -3.17 (0.28), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 247 
 HIS   0.007   0.001   HIS C 197 
 PHE   0.025   0.002   PHE D  78 
 TYR   0.021   0.002   TYR C 218 
 ARG   0.006   0.001   ARG A 342 

*********************** 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
  186 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 184
  time to evaluate  : 1.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  290 ASN cc_start: 0.9019 (t0) cc_final: 0.8582 (p0)
REVERT: A  325 VAL cc_start: 0.9461 (t) cc_final: 0.9228 (t)
REVERT: B   93 MET cc_start: 0.9235 (mmt) cc_final: 0.8825 (mmm)
REVERT: B  172 LEU cc_start: 0.9568 (mm) cc_final: 0.9312 (mm)
REVERT: B  176 PHE cc_start: 0.9258 (t80) cc_final: 0.9022 (t80)
REVERT: B  177 PHE cc_start: 0.9338 (m-10) cc_final: 0.8835 (m-80)
REVERT: B  181 TYR cc_start: 0.9314 (t80) cc_final: 0.9032 (t80)
REVERT: B  385 ASP cc_start: 0.8345 (m-30) cc_final: 0.7296 (m-30)
REVERT: B  386 PHE cc_start: 0.9140 (t80) cc_final: 0.8538 (t80)
REVERT: B  388 PHE cc_start: 0.9460 (m-10) cc_final: 0.9195 (m-10)
REVERT: B  445 PHE cc_start: 0.9493 (m-80) cc_final: 0.9213 (m-80)
REVERT: C   40 PHE cc_start: 0.9602 (t80) cc_final: 0.9321 (t80)
REVERT: C   41 PHE cc_start: 0.9516 (m-80) cc_final: 0.9141 (m-10)
REVERT: C   90 TYR cc_start: 0.8924 (t80) cc_final: 0.8503 (t80)
REVERT: C   99 GLU cc_start: 0.8359 (pt0) cc_final: 0.8047 (pt0)
REVERT: C  119 TYR cc_start: 0.8922 (t80) cc_final: 0.8500 (t80)
REVERT: C  138 LEU cc_start: 0.9459 (mt) cc_final: 0.9241 (mt)
REVERT: C  218 TYR cc_start: 0.9492 (m-80) cc_final: 0.9169 (m-80)
REVERT: C  224 MET cc_start: 0.9468 (mmp) cc_final: 0.9238 (mmm)
REVERT: D   23 PHE cc_start: 0.8494 (m-80) cc_final: 0.8071 (m-80)
REVERT: D   56 TYR cc_start: 0.8919 (m-80) cc_final: 0.8671 (m-10)
REVERT: D   66 PHE cc_start: 0.9332 (t80) cc_final: 0.8956 (m-10)
REVERT: D   95 THR cc_start: 0.8173 (m) cc_final: 0.7665 (m)
  outliers start: 2
  outliers final: 1
  residues processed: 184
  average time/residue: 0.1798
  time to fit residues: 50.6839
Evaluate side-chains
  140 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 139
  time to evaluate  : 1.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 19 optimal weight:    8.9990
   chunk 128 optimal weight:    4.9990
   chunk 126 optimal weight:    9.9990
   chunk 77 optimal weight:    8.9990
   chunk 14 optimal weight:    1.9990
   chunk 71 optimal weight:   20.0000
   chunk 106 optimal weight:    6.9990
   chunk 40 optimal weight:    0.0060
   chunk 115 optimal weight:    9.9990
   chunk 54 optimal weight:   20.0000
   chunk 113 optimal weight:    5.9990
   overall best weight:    4.0004

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

Flipped N/Q/H residues before XYZ refinement:
A  74 HIS
A 142 ASN
A 220 HIS
** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 612 ASN
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 222 GLN
** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  68 GLN
** 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: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.049433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.042536 restraints weight = 80410.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.043652 restraints weight = 49381.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.044327 restraints weight = 33952.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.5583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  10555  Z= 0.296
  Angle     :  0.799  13.032  14399  Z= 0.413
  Chirality :  0.044   0.274   1678
  Planarity :  0.006   0.132   1792
  Dihedral  :  6.766  48.115   1416
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 17.65
  Ramachandran Plot:
    Outliers :  0.92 %
    Allowed  :  9.13 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  2.99 %
    Favored  : 96.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.56 %
    Twisted Proline : 3.51 %
    Twisted General : 0.48 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.24), residues: 1304
  helix:  1.21 (0.18), residues: 747
  sheet: -1.97 (0.45), residues: 118
  loop : -3.03 (0.29), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 247 
 HIS   0.009   0.002   HIS C 197 
 PHE   0.025   0.002   PHE B 465 
 TYR   0.025   0.002   TYR B 466 
 ARG   0.006   0.001   ARG D  82 

*********************** 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
  173 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 172
  time to evaluate  : 2.094 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 LYS cc_start: 0.9480 (mmtp) cc_final: 0.9215 (mtpp)
REVERT: A  290 ASN cc_start: 0.9056 (t0) cc_final: 0.8620 (p0)
REVERT: A  325 VAL cc_start: 0.9451 (t) cc_final: 0.9181 (t)
REVERT: A  343 MET cc_start: 0.9314 (tpt) cc_final: 0.8909 (tpt)
REVERT: B   93 MET cc_start: 0.9276 (mmt) cc_final: 0.8915 (mmp)
REVERT: B  106 TYR cc_start: 0.8941 (m-10) cc_final: 0.8216 (m-10)
REVERT: B  172 LEU cc_start: 0.9596 (mm) cc_final: 0.9343 (mm)
REVERT: B  177 PHE cc_start: 0.9370 (m-10) cc_final: 0.9150 (m-80)
REVERT: B  184 GLU cc_start: 0.9236 (mp0) cc_final: 0.8628 (mp0)
REVERT: B  385 ASP cc_start: 0.8364 (m-30) cc_final: 0.7166 (m-30)
REVERT: B  386 PHE cc_start: 0.9014 (t80) cc_final: 0.8510 (t80)
REVERT: B  388 PHE cc_start: 0.9451 (m-10) cc_final: 0.9171 (m-10)
REVERT: B  445 PHE cc_start: 0.9479 (m-80) cc_final: 0.9153 (m-80)
REVERT: C   40 PHE cc_start: 0.9632 (t80) cc_final: 0.9356 (t80)
REVERT: C   41 PHE cc_start: 0.9493 (m-80) cc_final: 0.9114 (m-10)
REVERT: C   90 TYR cc_start: 0.8973 (t80) cc_final: 0.8537 (t80)
REVERT: C   99 GLU cc_start: 0.8370 (pt0) cc_final: 0.8082 (pt0)
REVERT: C  119 TYR cc_start: 0.8914 (t80) cc_final: 0.8462 (t80)
REVERT: C  138 LEU cc_start: 0.9443 (mt) cc_final: 0.9242 (mt)
REVERT: C  218 TYR cc_start: 0.9517 (m-80) cc_final: 0.9182 (m-10)
REVERT: C  224 MET cc_start: 0.9496 (mmp) cc_final: 0.9264 (mmm)
REVERT: D   23 PHE cc_start: 0.8638 (m-80) cc_final: 0.8115 (m-80)
REVERT: D   56 TYR cc_start: 0.9070 (m-80) cc_final: 0.8724 (m-10)
REVERT: D   66 PHE cc_start: 0.9367 (t80) cc_final: 0.9055 (m-10)
REVERT: D   95 THR cc_start: 0.8259 (m) cc_final: 0.7637 (m)
  outliers start: 1
  outliers final: 0
  residues processed: 172
  average time/residue: 0.1987
  time to fit residues: 51.8635
Evaluate side-chains
  131 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 1.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 91 optimal weight:    5.9990
   chunk 59 optimal weight:    9.9990
   chunk 113 optimal weight:   10.0000
   chunk 114 optimal weight:    7.9990
   chunk 109 optimal weight:    5.9990
   chunk 126 optimal weight:    8.9990
   chunk 22 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   chunk 51 optimal weight:    9.9990
   chunk 23 optimal weight:   10.0000
   chunk 20 optimal weight:    0.9980
   overall best weight:    4.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 237 GLN
A 305 GLN
** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 610 HIS
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 464 GLN ** 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.048703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.041853 restraints weight = 79711.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.042937 restraints weight = 51061.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.043611 restraints weight = 35347.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.5815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.076  10555  Z= 0.343
  Angle     :  0.815  12.353  14399  Z= 0.423
  Chirality :  0.044   0.272   1678
  Planarity :  0.006   0.123   1792
  Dihedral  :  6.695  48.224   1416
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 19.35
  Ramachandran Plot:
    Outliers :  0.92 %
    Allowed  :  9.51 %
    Favored  : 89.57 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.23), residues: 1304
  helix:  1.05 (0.18), residues: 752
  sheet: -2.11 (0.44), residues: 116
  loop : -3.01 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP D  36 
 HIS   0.012   0.002   HIS C 197 
 PHE   0.028   0.002   PHE C 132 
 TYR   0.025   0.002   TYR D  18 
 ARG   0.005   0.001   ARG A 342 

*********************** 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
  165 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 1.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  215 MET cc_start: 0.9255 (mtm) cc_final: 0.8795 (mmm)
REVERT: A  290 ASN cc_start: 0.9170 (t0) cc_final: 0.8575 (t0)
REVERT: A  305 GLN cc_start: 0.9235 (tp-100) cc_final: 0.8965 (tt0)
REVERT: B   93 MET cc_start: 0.9289 (mmt) cc_final: 0.8933 (mmp)
REVERT: B  106 TYR cc_start: 0.8962 (m-10) cc_final: 0.8588 (m-10)
REVERT: B  172 LEU cc_start: 0.9602 (mm) cc_final: 0.9351 (mm)
REVERT: B  385 ASP cc_start: 0.8464 (m-30) cc_final: 0.7570 (m-30)
REVERT: B  386 PHE cc_start: 0.9039 (t80) cc_final: 0.8546 (t80)
REVERT: B  388 PHE cc_start: 0.9394 (m-10) cc_final: 0.9097 (m-10)
REVERT: B  445 PHE cc_start: 0.9464 (m-80) cc_final: 0.9094 (m-80)
REVERT: C   40 PHE cc_start: 0.9669 (t80) cc_final: 0.9360 (t80)
REVERT: C   41 PHE cc_start: 0.9441 (m-80) cc_final: 0.9075 (m-10)
REVERT: C   90 TYR cc_start: 0.9021 (t80) cc_final: 0.8528 (t80)
REVERT: C   99 GLU cc_start: 0.8353 (pt0) cc_final: 0.7978 (pt0)
REVERT: C  119 TYR cc_start: 0.8925 (t80) cc_final: 0.8444 (t80)
REVERT: C  128 ILE cc_start: 0.9264 (tp) cc_final: 0.8936 (tp)
REVERT: C  132 PHE cc_start: 0.8611 (m-10) cc_final: 0.8384 (m-80)
REVERT: C  178 PHE cc_start: 0.9437 (t80) cc_final: 0.9200 (t80)
REVERT: C  218 TYR cc_start: 0.9568 (m-80) cc_final: 0.9306 (m-80)
REVERT: C  224 MET cc_start: 0.9503 (mmp) cc_final: 0.9232 (mmm)
REVERT: D   23 PHE cc_start: 0.8662 (m-80) cc_final: 0.8073 (m-80)
REVERT: D   56 TYR cc_start: 0.9063 (m-80) cc_final: 0.8828 (m-80)
REVERT: D   66 PHE cc_start: 0.9298 (t80) cc_final: 0.9065 (m-10)
REVERT: D   95 THR cc_start: 0.8232 (m) cc_final: 0.7503 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 0.1692
  time to fit residues: 43.3880
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  : 1.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 83 optimal weight:    0.9990
   chunk 106 optimal weight:    0.9990
   chunk 86 optimal weight:    0.7980
   chunk 67 optimal weight:    0.4980
   chunk 75 optimal weight:    0.9980
   chunk 33 optimal weight:    9.9990
   chunk 47 optimal weight:    9.9990
   chunk 17 optimal weight:    0.0010
   chunk 25 optimal weight:    6.9990
   chunk 118 optimal weight:    0.9980
   chunk 68 optimal weight:    5.9990
   overall best weight:    0.6586

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

Flipped N/Q/H residues before XYZ refinement:
A 305 GLN
A 531 ASN
A 562 ASN
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.050997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.043974 restraints weight = 75190.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.045094 restraints weight = 46724.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.045773 restraints weight = 32639.968|
|-----------------------------------------------------------------------------|
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.6090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063  10555  Z= 0.203
  Angle     :  0.781  14.285  14399  Z= 0.397
  Chirality :  0.044   0.292   1678
  Planarity :  0.006   0.144   1792
  Dihedral  :  6.377  44.926   1416
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 15.86
  Ramachandran Plot:
    Outliers :  0.92 %
    Allowed  :  7.90 %
    Favored  : 91.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.48 %
    Twisted Proline : 1.75 %
    Twisted General : 0.48 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.24), residues: 1304
  helix:  1.31 (0.18), residues: 745
  sheet: -1.77 (0.46), residues: 117
  loop : -2.95 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 247 
 HIS   0.005   0.001   HIS C 197 
 PHE   0.030   0.002   PHE B  86 
 TYR   0.022   0.002   TYR A 554 
 ARG   0.007   0.001   ARG A 342 

*********************** 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
  188 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 1.151 
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  215 MET cc_start: 0.9188 (mtm) cc_final: 0.8811 (mmm)
REVERT: A  290 ASN cc_start: 0.9217 (t0) cc_final: 0.8675 (t0)
REVERT: A  325 VAL cc_start: 0.9482 (t) cc_final: 0.9258 (t)
REVERT: A  343 MET cc_start: 0.9079 (tpt) cc_final: 0.8860 (tpt)
REVERT: B   93 MET cc_start: 0.9250 (mmt) cc_final: 0.8991 (mmp)
REVERT: B  106 TYR cc_start: 0.8821 (m-10) cc_final: 0.8420 (m-10)
REVERT: B  172 LEU cc_start: 0.9562 (mm) cc_final: 0.9308 (mm)
REVERT: B  176 PHE cc_start: 0.9262 (t80) cc_final: 0.9034 (t80)
REVERT: B  177 PHE cc_start: 0.9271 (m-80) cc_final: 0.8639 (m-80)
REVERT: B  211 ILE cc_start: 0.9595 (tp) cc_final: 0.9239 (tp)
REVERT: B  385 ASP cc_start: 0.8189 (m-30) cc_final: 0.6937 (m-30)
REVERT: B  386 PHE cc_start: 0.9087 (t80) cc_final: 0.8531 (t80)
REVERT: B  388 PHE cc_start: 0.9363 (m-10) cc_final: 0.8958 (m-80)
REVERT: B  422 LEU cc_start: 0.9496 (mt) cc_final: 0.9248 (pp)
REVERT: B  445 PHE cc_start: 0.9489 (m-80) cc_final: 0.9191 (m-80)
REVERT: B  463 HIS cc_start: 0.8928 (m90) cc_final: 0.8480 (m-70)
REVERT: C   35 LEU cc_start: 0.9597 (tt) cc_final: 0.9354 (mm)
REVERT: C   40 PHE cc_start: 0.9577 (t80) cc_final: 0.9307 (t80)
REVERT: C   41 PHE cc_start: 0.9406 (m-80) cc_final: 0.9047 (m-10)
REVERT: C   90 TYR cc_start: 0.8862 (t80) cc_final: 0.8388 (t80)
REVERT: C   99 GLU cc_start: 0.8336 (pt0) cc_final: 0.7923 (pt0)
REVERT: C  205 PHE cc_start: 0.8036 (m-10) cc_final: 0.7762 (m-80)
REVERT: C  218 TYR cc_start: 0.9562 (m-80) cc_final: 0.9296 (m-10)
REVERT: C  224 MET cc_start: 0.9447 (mmp) cc_final: 0.9172 (mmm)
REVERT: D   23 PHE cc_start: 0.8660 (m-80) cc_final: 0.8141 (m-80)
REVERT: D   56 TYR cc_start: 0.9031 (m-80) cc_final: 0.8776 (m-80)
REVERT: D   66 PHE cc_start: 0.9303 (t80) cc_final: 0.9070 (m-10)
REVERT: D   95 THR cc_start: 0.8144 (m) cc_final: 0.7776 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 188
  average time/residue: 0.1846
  time to fit residues: 53.5104
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  : 1.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 72 optimal weight:    6.9990
   chunk 58 optimal weight:    7.9990
   chunk 94 optimal weight:    2.9990
   chunk 60 optimal weight:   10.0000
   chunk 61 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9990
   chunk 89 optimal weight:    2.9990
   chunk 109 optimal weight:   10.0000
   chunk 98 optimal weight:    0.8980
   chunk 25 optimal weight:    8.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 459 GLN
** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  83 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.049430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.042770 restraints weight = 77580.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.043819 restraints weight = 50980.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.044447 restraints weight = 35796.713|
|-----------------------------------------------------------------------------|
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.6246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  10555  Z= 0.249
  Angle     :  0.776  12.348  14399  Z= 0.396
  Chirality :  0.044   0.287   1678
  Planarity :  0.006   0.132   1792
  Dihedral  :  6.269  45.537   1416
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 17.56
  Ramachandran Plot:
    Outliers :  1.00 %
    Allowed  :  8.59 %
    Favored  : 90.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.56 %
    Twisted Proline : 1.75 %
    Twisted General : 0.32 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.24), residues: 1304
  helix:  1.20 (0.18), residues: 749
  sheet: -1.82 (0.45), residues: 117
  loop : -2.92 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP B 247 
 HIS   0.008   0.001   HIS C  58 
 PHE   0.031   0.002   PHE C 132 
 TYR   0.019   0.002   TYR B 446 
 ARG   0.005   0.001   ARG A 342 

*********************** 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
  170 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 1.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  215 MET cc_start: 0.9194 (mtm) cc_final: 0.8893 (mmm)
REVERT: A  290 ASN cc_start: 0.9200 (t0) cc_final: 0.8637 (t0)
REVERT: B   93 MET cc_start: 0.9273 (mmt) cc_final: 0.9005 (mmp)
REVERT: B  106 TYR cc_start: 0.8891 (m-10) cc_final: 0.7903 (m-10)
REVERT: B  172 LEU cc_start: 0.9642 (mm) cc_final: 0.9345 (mm)
REVERT: B  176 PHE cc_start: 0.9322 (t80) cc_final: 0.9069 (t80)
REVERT: B  177 PHE cc_start: 0.9428 (m-80) cc_final: 0.8977 (m-80)
REVERT: B  184 GLU cc_start: 0.9375 (mp0) cc_final: 0.8648 (mp0)
REVERT: B  210 MET cc_start: 0.8332 (ppp) cc_final: 0.8013 (ppp)
REVERT: B  385 ASP cc_start: 0.8273 (m-30) cc_final: 0.7147 (m-30)
REVERT: B  386 PHE cc_start: 0.9029 (t80) cc_final: 0.8502 (t80)
REVERT: B  388 PHE cc_start: 0.9331 (m-10) cc_final: 0.8896 (m-10)
REVERT: B  463 HIS cc_start: 0.8902 (m90) cc_final: 0.8460 (m-70)
REVERT: C   35 LEU cc_start: 0.9605 (tt) cc_final: 0.9349 (mm)
REVERT: C   40 PHE cc_start: 0.9618 (t80) cc_final: 0.9244 (t80)
REVERT: C   41 PHE cc_start: 0.9475 (m-80) cc_final: 0.9103 (m-10)
REVERT: C   90 TYR cc_start: 0.8926 (t80) cc_final: 0.8448 (t80)
REVERT: C   99 GLU cc_start: 0.8344 (pt0) cc_final: 0.7955 (pt0)
REVERT: C  218 TYR cc_start: 0.9567 (m-80) cc_final: 0.9217 (m-10)
REVERT: C  224 MET cc_start: 0.9464 (mmp) cc_final: 0.9166 (mmm)
REVERT: D   23 PHE cc_start: 0.8603 (m-80) cc_final: 0.8127 (m-80)
REVERT: D   56 TYR cc_start: 0.9046 (m-80) cc_final: 0.8796 (m-80)
REVERT: D   66 PHE cc_start: 0.9352 (t80) cc_final: 0.9036 (m-10)
REVERT: D   95 THR cc_start: 0.8066 (m) cc_final: 0.7261 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 170
  average time/residue: 0.1795
  time to fit residues: 47.0532
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  : 1.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 101 optimal weight:   20.0000
   chunk 65 optimal weight:    4.9990
   chunk 92 optimal weight:    0.9980
   chunk 109 optimal weight:    6.9990
   chunk 76 optimal weight:    9.9990
   chunk 110 optimal weight:    5.9990
   chunk 49 optimal weight:    9.9990
   chunk 100 optimal weight:    4.9990
   chunk 34 optimal weight:    4.9990
   chunk 116 optimal weight:    5.9990
   chunk 69 optimal weight:    9.9990
   overall best weight:    4.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 531 ASN
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  83 GLN ** 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 = 0.3159 r_free = 0.3159 target = 0.048006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.041697 restraints weight = 78408.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.042619 restraints weight = 52103.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.043305 restraints weight = 37651.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.6309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.081  10555  Z= 0.313
  Angle     :  0.814  15.683  14399  Z= 0.417
  Chirality :  0.044   0.288   1678
  Planarity :  0.006   0.128   1792
  Dihedral  :  6.316  45.318   1416
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 19.50
  Ramachandran Plot:
    Outliers :  0.84 %
    Allowed  :  8.97 %
    Favored  : 90.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.51 %
    Cis-general     : 0.56 %
    Twisted Proline : 1.75 %
    Twisted General : 0.24 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (0.24), residues: 1304
  helix:  1.12 (0.18), residues: 746
  sheet: -2.07 (0.43), residues: 119
  loop : -2.92 (0.29), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP B 247 
 HIS   0.009   0.002   HIS C 171 
 PHE   0.022   0.002   PHE B 411 
 TYR   0.023   0.002   TYR A 196 
 ARG   0.004   0.001   ARG A 659 

********************** 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
  172 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 1.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  215 MET cc_start: 0.9234 (mtm) cc_final: 0.8741 (mmm)
REVERT: A  290 ASN cc_start: 0.9196 (t0) cc_final: 0.8714 (t0)
REVERT: B   93 MET cc_start: 0.9301 (mmt) cc_final: 0.8927 (mmp)
REVERT: B  106 TYR cc_start: 0.8828 (m-10) cc_final: 0.8176 (m-10)
REVERT: B  168 ILE cc_start: 0.9401 (mm) cc_final: 0.9132 (mt)
REVERT: B  172 LEU cc_start: 0.9626 (mm) cc_final: 0.9337 (mm)
REVERT: B  176 PHE cc_start: 0.9385 (t80) cc_final: 0.8910 (t80)
REVERT: B  177 PHE cc_start: 0.9426 (m-80) cc_final: 0.8950 (m-80)
REVERT: B  184 GLU cc_start: 0.9381 (mp0) cc_final: 0.8657 (mp0)
REVERT: B  211 ILE cc_start: 0.9621 (tp) cc_final: 0.9416 (tp)
REVERT: B  385 ASP cc_start: 0.8438 (m-30) cc_final: 0.7576 (m-30)
REVERT: B  386 PHE cc_start: 0.9077 (t80) cc_final: 0.8560 (t80)
REVERT: B  388 PHE cc_start: 0.9341 (m-10) cc_final: 0.8938 (m-10)
REVERT: B  463 HIS cc_start: 0.8939 (m90) cc_final: 0.8481 (m90)
REVERT: C   40 PHE cc_start: 0.9622 (t80) cc_final: 0.9241 (t80)
REVERT: C   41 PHE cc_start: 0.9468 (m-80) cc_final: 0.9071 (m-10)
REVERT: C   90 TYR cc_start: 0.8988 (t80) cc_final: 0.8438 (t80)
REVERT: C  224 MET cc_start: 0.9488 (mmp) cc_final: 0.9182 (mmm)
REVERT: D   23 PHE cc_start: 0.8634 (m-80) cc_final: 0.8062 (m-80)
REVERT: D   56 TYR cc_start: 0.8968 (m-80) cc_final: 0.8702 (m-80)
REVERT: D   95 THR cc_start: 0.8169 (m) cc_final: 0.7177 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 172
  average time/residue: 0.1812
  time to fit residues: 47.8325
Evaluate side-chains
  128 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 1.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 101 optimal weight:   20.0000
   chunk 53 optimal weight:    9.9990
   chunk 4 optimal weight:    0.5980
   chunk 95 optimal weight:   10.0000
   chunk 42 optimal weight:    4.9990
   chunk 54 optimal weight:    5.9990
   chunk 59 optimal weight:    8.9990
   chunk 35 optimal weight:    0.9980
   chunk 47 optimal weight:    9.9990
   chunk 107 optimal weight:    0.7980
   overall best weight:    2.6784

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

Flipped N/Q/H residues before XYZ refinement:
A 199 HIS
A 449 HIS
** A 454 GLN ** 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  83 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 = 0.3179 r_free = 0.3179 target = 0.048893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.042399 restraints weight = 77693.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.043381 restraints weight = 51367.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.043927 restraints weight = 37603.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.6453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078  10555  Z= 0.243
  Angle     :  0.780  12.553  14399  Z= 0.396
  Chirality :  0.044   0.279   1678
  Planarity :  0.006   0.124   1792
  Dihedral  :  6.193  44.711   1416
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 17.95
  Ramachandran Plot:
    Outliers :  0.84 %
    Allowed  :  8.97 %
    Favored  : 90.18 %
  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 : 0.16 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.24), residues: 1304
  helix:  1.13 (0.18), residues: 747
  sheet: -2.12 (0.42), residues: 119
  loop : -2.82 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP B 247 
 HIS   0.007   0.001   HIS C  58 
 PHE   0.051   0.002   PHE A 682 
 TYR   0.021   0.002   TYR D  18 
 ARG   0.005   0.001   ARG A 342 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2743.35 seconds
wall clock time: 50 minutes 28.92 seconds (3028.92 seconds total)