Starting phenix.real_space_refine
on Fri Oct 10 16:10:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5uz7_8623/10_2025/5uz7_8623.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5uz7_8623/10_2025/5uz7_8623.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/5uz7_8623/10_2025/5uz7_8623.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5uz7_8623/10_2025/5uz7_8623.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5uz7_8623/10_2025/5uz7_8623.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5uz7_8623/10_2025/5uz7_8623.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.008
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      53      5.16       5
     C    4877      2.51       5
     N    1334      2.21       5
     O    1379      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7643
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1566
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 185, 1566
          Classifications: {'peptide': 185}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 4, 'TRANS': 180}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 16
    Chain: "B"
      Number of atoms: 2579
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2579
          Classifications: {'peptide': 340}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 28
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 30
    Chain: "G"
      Number of atoms: 420
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 420
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "N"
      Number of atoms: 972
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 972
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "R"
      Number of atoms: 2106
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 266, 2106
          Classifications: {'peptide': 266}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PTRANS': 7, 'TRANS': 258}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 118
          Unresolved non-hydrogen angles: 151
          Unresolved non-hydrogen dihedrals: 101
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLU:plan': 3, 'TYR:plan': 1, 'PHE:plan': 2, 'ARG:plan': 5, 'ASP:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 86
  Time building chain proxies: 2.01, per 1000 atoms: 0.26
  Number of scatterers: 7643
  At special positions: 0
  Unit cell: (130.38, 95.4, 98.58, 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      53     16.00
     O    1379      8.00
     N    1334      7.00
     C    4877      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.02
    Simple disulfide: pdb=" SG  CYS R 219 " - pdb=" SG  CYS R 289 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.64
  Conformation dependent library (CDL) restraints added in 485.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1834

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 10 sheets defined
      40.6% alpha, 18.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 39
      removed outlier: 3.736A  pdb=" N   GLU A  21 " --> pdb=" O   LYS A  17 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ALA A  39 " --> pdb=" O   GLN A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 312 through 316
      removed outlier: 3.537A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 353
      removed outlier: 3.893A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   SER A 349 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 391
      removed outlier: 3.807A  pdb=" N   TYR A 391 " --> pdb=" O   HIS A 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 25
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.866A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 10 through 13
    Processing helix  chain 'G' and resid 14 through 24
      removed outlier: 4.146A  pdb=" N   GLN G  18 " --> pdb=" O   LYS G  14 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.721A  pdb=" N   ALA G  35 " --> pdb=" O   SER G  31 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ASP G  36 " --> pdb=" O   LYS G  32 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.531A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 4.097A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 137 through 173
    Processing helix  chain 'R' and resid 178 through 205
      removed outlier: 3.653A  pdb=" N   LEU R 183 " --> pdb=" O   GLN R 179 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 215 through 250
    Processing helix  chain 'R' and resid 258 through 268
      removed outlier: 3.879A  pdb=" N   TYR R 262 " --> pdb=" O   ARG R 258 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 270 through 285
    Processing helix  chain 'R' and resid 298 through 326
      Proline residue:  R 304  - end of helix
    Processing helix  chain 'R' and resid 338 through 349
    Processing helix  chain 'R' and resid 350 through 353
    Processing helix  chain 'R' and resid 354 through 359
    Processing helix  chain 'R' and resid 367 through 382
    Processing helix  chain 'R' and resid 382 through 393
    Processing helix  chain 'R' and resid 395 through 418
    Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 214
      removed outlier: 3.565A  pdb=" N   HIS A 220 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 10.073A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.584A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.372A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.629A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.851A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   THR B 329 " --> pdb=" O   LYS B 337 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 62
      removed outlier: 6.582A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.932A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.710A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151
      removed outlier: 3.646A  pdb=" N   CYS B 166 " --> pdb=" O   PHE B 180 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 190 through 192
      removed outlier: 4.081A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.239A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 232 through 234
      removed outlier: 3.873A  pdb=" N   LEU B 252 " --> pdb=" O   MET B 262 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278
      removed outlier: 3.775A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 8
    Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12
      removed outlier: 7.045A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    398 hydrogen bonds defined for protein.
    1149 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: 0.99

  Time building geometry restraints manager: 0.80 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2427
        1.34 -     1.46: 1850
        1.46 -     1.58: 3453
        1.58 -     1.70: 0
        1.70 -     1.82: 76
  Bond restraints: 7806
  Sorted by residual:
  bond pdb=" C   VAL R 349 "
       pdb=" N   PRO R 350 "
    ideal  model  delta    sigma   weight residual
    1.334  1.434 -0.100 2.34e-02 1.83e+03 1.82e+01
  bond pdb=" CB  VAL N  48 "
       pdb=" CG2 VAL N  48 "
    ideal  model  delta    sigma   weight residual
    1.521  1.444  0.077 3.30e-02 9.18e+02 5.44e+00
  bond pdb=" CG  LEU B  14 "
       pdb=" CD2 LEU B  14 "
    ideal  model  delta    sigma   weight residual
    1.521  1.460  0.061 3.30e-02 9.18e+02 3.45e+00
  bond pdb=" CB  PRO R 350 "
       pdb=" CG  PRO R 350 "
    ideal  model  delta    sigma   weight residual
    1.492  1.403  0.089 5.00e-02 4.00e+02 3.18e+00
  bond pdb=" CB  CYS B 204 "
       pdb=" SG  CYS B 204 "
    ideal  model  delta    sigma   weight residual
    1.808  1.752  0.056 3.30e-02 9.18e+02 2.90e+00
  ... (remaining 7801 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.12: 10313
        3.12 -     6.25: 220
        6.25 -     9.37: 30
        9.37 -    12.50: 12
       12.50 -    15.62: 3
  Bond angle restraints: 10578
  Sorted by residual:
  angle pdb=" C   ILE R 248 "
        pdb=" N   VAL R 249 "
        pdb=" CA  VAL R 249 "
      ideal   model   delta    sigma   weight residual
     121.71  113.62    8.09 1.20e+00 6.94e-01 4.54e+01
  angle pdb=" CA  LEU B  79 "
        pdb=" CB  LEU B  79 "
        pdb=" CG  LEU B  79 "
      ideal   model   delta    sigma   weight residual
     116.30  131.92  -15.62 3.50e+00 8.16e-02 1.99e+01
  angle pdb=" CA  LEU R 142 "
        pdb=" CB  LEU R 142 "
        pdb=" CG  LEU R 142 "
      ideal   model   delta    sigma   weight residual
     116.30  131.60  -15.30 3.50e+00 8.16e-02 1.91e+01
  angle pdb=" CA  GLU A 392 "
        pdb=" CB  GLU A 392 "
        pdb=" CG  GLU A 392 "
      ideal   model   delta    sigma   weight residual
     114.10  122.40   -8.30 2.00e+00 2.50e-01 1.72e+01
  angle pdb=" C   THR N 113 "
        pdb=" N   THR N 114 "
        pdb=" CA  THR N 114 "
      ideal   model   delta    sigma   weight residual
     122.61  128.81   -6.20 1.56e+00 4.11e-01 1.58e+01
  ... (remaining 10573 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.98: 4286
       15.98 -    31.95: 263
       31.95 -    47.93: 40
       47.93 -    63.90: 7
       63.90 -    79.88: 5
  Dihedral angle restraints: 4601
    sinusoidal: 1769
      harmonic: 2832
  Sorted by residual:
  dihedral pdb=" CA  THR N 113 "
           pdb=" C   THR N 113 "
           pdb=" N   THR N 114 "
           pdb=" CA  THR N 114 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.99   29.01     0      5.00e+00 4.00e-02 3.37e+01
  dihedral pdb=" CA  THR B 165 "
           pdb=" C   THR B 165 "
           pdb=" N   CYS B 166 "
           pdb=" CA  CYS B 166 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.16   24.84     0      5.00e+00 4.00e-02 2.47e+01
  dihedral pdb=" CA  LYS R 326 "
           pdb=" C   LYS R 326 "
           pdb=" N   MET R 327 "
           pdb=" CA  MET R 327 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.89   22.11     0      5.00e+00 4.00e-02 1.96e+01
  ... (remaining 4598 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 804
       0.057 -    0.114: 299
       0.114 -    0.171: 74
       0.171 -    0.228: 13
       0.228 -    0.285: 4
  Chirality restraints: 1194
  Sorted by residual:
  chirality pdb=" CB  VAL A 241 "
            pdb=" CA  VAL A 241 "
            pdb=" CG1 VAL A 241 "
            pdb=" CG2 VAL A 241 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.34   -0.28 2.00e-01 2.50e+01 2.03e+00
  chirality pdb=" CG  LEU R 238 "
            pdb=" CB  LEU R 238 "
            pdb=" CD1 LEU R 238 "
            pdb=" CD2 LEU R 238 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.32   -0.27 2.00e-01 2.50e+01 1.82e+00
  chirality pdb=" CB  VAL N 110 "
            pdb=" CA  VAL N 110 "
            pdb=" CG1 VAL N 110 "
            pdb=" CG2 VAL N 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.43e+00
  ... (remaining 1191 not shown)

  Planarity restraints: 1340
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY R 303 "   -0.054 5.00e-02 4.00e+02   8.22e-02 1.08e+01
        pdb=" N   PRO R 304 "    0.142 5.00e-02 4.00e+02
        pdb=" CA  PRO R 304 "   -0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO R 304 "   -0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR R 138 "    0.053 5.00e-02 4.00e+02   8.02e-02 1.03e+01
        pdb=" N   PRO R 139 "   -0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO R 139 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO R 139 "    0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 332 "    0.017 2.00e-02 2.50e+03   1.81e-02 8.19e+00
        pdb=" CG  TRP B 332 "   -0.049 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 332 "    0.023 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 332 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 332 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 332 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 332 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 332 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 332 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 332 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1337 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 1941
        2.79 -     3.32: 6949
        3.32 -     3.85: 12554
        3.85 -     4.37: 14079
        4.37 -     4.90: 24743
  Nonbonded interactions: 60266
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" OG  SER B 147 "
            pdb=" OG  SER B 160 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" OE1 GLN A 384 "
            pdb=" NZ  LYS R 326 "
     model   vdw
     2.308 3.120
  nonbonded pdb=" O   CYS B 204 "
            pdb=" OH  TYR N 117 "
     model   vdw
     2.321 3.040
  nonbonded pdb=" O   CYS N  22 "
            pdb=" OG1 THR N  78 "
     model   vdw
     2.322 3.040
  ... (remaining 60261 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:             0.540
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.630
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
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      :  0.008   0.100   7809  Z= 0.332
  Angle     :  1.175  15.623  10584  Z= 0.612
  Chirality :  0.063   0.285   1194
  Planarity :  0.008   0.082   1340
  Dihedral  : 11.044  79.876   2758
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  6.34 %
    Favored  : 93.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.30 (0.24), residues: 948
  helix: -1.12 (0.23), residues: 363
  sheet: -0.53 (0.33), residues: 220
  loop : -2.49 (0.26), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG N 118 
 TYR   0.043   0.004   TYR R 372 
 PHE   0.037   0.003   PHE B 151 
 TRP   0.049   0.005   TRP B 332 
 HIS   0.019   0.003   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00751 ( 7806)
  covalent geometry    : angle       1.17357 (10578)
  SS BOND              : bond        0.00782 (    3)
  SS BOND              : angle       2.32009 (    6)
  hydrogen bonds       : bond        0.10583 (  398)
  hydrogen bonds       : angle       9.52347 ( 1149)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  347 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 344
  time to evaluate  : 0.295 
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   20 ARG cc_start: 0.8476 (mtt180) cc_final: 0.8114 (mtt-85)
REVERT: A   24 LYS cc_start: 0.8910 (mttt) cc_final: 0.8636 (mtmt)
REVERT: A   29 GLN cc_start: 0.8961 (tt0) cc_final: 0.8616 (tm-30)
REVERT: A   32 LYS cc_start: 0.9471 (mttt) cc_final: 0.9014 (mmtt)
REVERT: A  222 PHE cc_start: 0.8040 (t80) cc_final: 0.7659 (t80)
REVERT: A  272 LEU cc_start: 0.9161 (tp) cc_final: 0.8806 (tp)
REVERT: A  281 TRP cc_start: 0.8071 (m100) cc_final: 0.7864 (m100)
REVERT: A  340 PHE cc_start: 0.8411 (t80) cc_final: 0.8063 (t80)
REVERT: B  127 LYS cc_start: 0.8563 (ptmm) cc_final: 0.8027 (ptmm)
REVERT: B  145 TYR cc_start: 0.8989 (p90) cc_final: 0.8755 (p90)
REVERT: B  188 MET cc_start: 0.8522 (mmm) cc_final: 0.8232 (mmt)
REVERT: B  325 MET cc_start: 0.8471 (tpp) cc_final: 0.7820 (tpt)
REVERT: G   18 GLN cc_start: 0.7087 (mm-40) cc_final: 0.6790 (mm-40)
REVERT: R  262 TYR cc_start: 0.8175 (m-80) cc_final: 0.7953 (m-80)
REVERT: R  328 ARG cc_start: 0.7640 (tpm170) cc_final: 0.7416 (mtp85)
REVERT: R  342 VAL cc_start: 0.8536 (p) cc_final: 0.8209 (p)
REVERT: R  352 LEU cc_start: 0.7715 (pt) cc_final: 0.7379 (pt)
  outliers start: 3
  outliers final: 0
  residues processed: 347
  average time/residue: 0.1054
  time to fit residues: 47.4221
Evaluate side-chains
  230 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0770
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.7138

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
A 377 ASN
A 390 GLN
B  36 ASN
B 259 GLN
B 340 ASN
G  24 ASN
G  44 HIS
R 186 ASN
R 194 ASN
R 233 ASN
** R 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 415 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.133019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.108752 restraints weight = 13441.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.111575 restraints weight = 8006.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.113424 restraints weight = 5587.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.114880 restraints weight = 4342.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.115647 restraints weight = 3593.466|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.2899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7809  Z= 0.145
  Angle     :  0.712   9.766  10584  Z= 0.367
  Chirality :  0.044   0.180   1194
  Planarity :  0.005   0.063   1340
  Dihedral  :  5.253  23.725   1054
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  2.24 %
    Favored  : 97.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.03 (0.26), residues: 948
  helix:  0.44 (0.25), residues: 364
  sheet: -0.41 (0.34), residues: 225
  loop : -2.01 (0.29), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG R 281 
 TYR   0.021   0.002   TYR A 360 
 PHE   0.026   0.001   PHE R 314 
 TRP   0.022   0.002   TRP B  82 
 HIS   0.009   0.001   HIS R 377 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 7806)
  covalent geometry    : angle       0.71127 (10578)
  SS BOND              : bond        0.00128 (    3)
  SS BOND              : angle       1.31674 (    6)
  hydrogen bonds       : bond        0.04504 (  398)
  hydrogen bonds       : angle       6.12609 ( 1149)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 308
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 LYS cc_start: 0.8598 (tttt) cc_final: 0.8354 (tppt)
REVERT: A   35 GLN cc_start: 0.8314 (pt0) cc_final: 0.7774 (pp30)
REVERT: A  342 ARG cc_start: 0.7040 (ttt180) cc_final: 0.6832 (ptm-80)
REVERT: A  357 HIS cc_start: 0.7716 (p-80) cc_final: 0.7083 (p-80)
REVERT: A  389 ARG cc_start: 0.8056 (ttm110) cc_final: 0.7596 (ttm110)
REVERT: B   13 GLN cc_start: 0.7936 (pp30) cc_final: 0.7633 (pp30)
REVERT: B   75 GLN cc_start: 0.8069 (tm-30) cc_final: 0.7797 (tm-30)
REVERT: B  127 LYS cc_start: 0.7836 (ptmm) cc_final: 0.7381 (ptmm)
REVERT: B  226 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7505 (mm-30)
REVERT: B  254 ASP cc_start: 0.7983 (t70) cc_final: 0.7696 (t0)
REVERT: N    5 GLN cc_start: 0.7084 (tp-100) cc_final: 0.6881 (tm-30)
REVERT: R  197 ILE cc_start: 0.9045 (tt) cc_final: 0.8672 (tt)
REVERT: R  204 GLU cc_start: 0.7733 (tt0) cc_final: 0.7430 (mt-10)
REVERT: R  273 PRO cc_start: 0.9246 (Cg_exo) cc_final: 0.9044 (Cg_endo)
REVERT: R  406 TRP cc_start: 0.7913 (t60) cc_final: 0.6763 (t60)
  outliers start: 2
  outliers final: 1
  residues processed: 309
  average time/residue: 0.0993
  time to fit residues: 39.9878
Evaluate side-chains
  234 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 233
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0980
   chunk 39 optimal weight:    5.9990
   chunk 84 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 61 optimal weight:    6.9990
   chunk 28 optimal weight:    3.9990
   chunk 48 optimal weight:   10.0000
   chunk 80 optimal weight:   10.0000
   chunk 90 optimal weight:    7.9990
   overall best weight:    3.0188

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

Flipped N/Q/H residues before XYZ refinement:
A 377 ASN
B 142 HIS
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 194 ASN
** R 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 415 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.125020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.100925 restraints weight = 13923.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.103535 restraints weight = 8471.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.105322 restraints weight = 5982.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.106400 restraints weight = 4705.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.107370 restraints weight = 3997.703|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.3587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   7809  Z= 0.240
  Angle     :  0.743  12.031  10584  Z= 0.384
  Chirality :  0.047   0.166   1194
  Planarity :  0.005   0.059   1340
  Dihedral  :  5.203  23.043   1054
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 12.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.73 %
    Favored  : 96.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.03 (0.26), residues: 948
  helix:  0.68 (0.26), residues: 368
  sheet: -0.87 (0.34), residues: 225
  loop : -1.96 (0.29), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 197 
 TYR   0.015   0.002   TYR R 374 
 PHE   0.025   0.002   PHE R 314 
 TRP   0.019   0.002   TRP B  82 
 HIS   0.011   0.002   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00532 ( 7806)
  covalent geometry    : angle       0.74256 (10578)
  SS BOND              : bond        0.01121 (    3)
  SS BOND              : angle       0.90403 (    6)
  hydrogen bonds       : bond        0.04507 (  398)
  hydrogen bonds       : angle       5.67356 ( 1149)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 266
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 GLN cc_start: 0.8143 (pt0) cc_final: 0.7902 (pp30)
REVERT: A  389 ARG cc_start: 0.8040 (ttm110) cc_final: 0.7695 (ttm110)
REVERT: B   55 LEU cc_start: 0.8911 (mp) cc_final: 0.8655 (mp)
REVERT: B  127 LYS cc_start: 0.7966 (ptmm) cc_final: 0.7457 (ptmm)
REVERT: B  156 GLN cc_start: 0.8026 (pt0) cc_final: 0.7811 (pt0)
REVERT: B  171 ILE cc_start: 0.7871 (mm) cc_final: 0.7568 (mm)
REVERT: B  254 ASP cc_start: 0.8124 (t70) cc_final: 0.7840 (t70)
REVERT: G   22 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7676 (tm-30)
REVERT: R  204 GLU cc_start: 0.7788 (tt0) cc_final: 0.7393 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 267
  average time/residue: 0.1013
  time to fit residues: 35.4282
Evaluate side-chains
  221 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 221
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 72 optimal weight:    6.9990
   chunk 29 optimal weight:    5.9990
   chunk 90 optimal weight:    0.9980
   chunk 64 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 50 optimal weight:    5.9990
   chunk 31 optimal weight:    6.9990
   chunk 74 optimal weight:    0.7980
   chunk 41 optimal weight:    0.8980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 408 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.126891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.103769 restraints weight = 14168.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.106621 restraints weight = 8158.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.108643 restraints weight = 5543.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.110048 restraints weight = 4207.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.110674 restraints weight = 3459.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.3922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7809  Z= 0.140
  Angle     :  0.711  10.332  10584  Z= 0.357
  Chirality :  0.045   0.280   1194
  Planarity :  0.005   0.052   1340
  Dihedral  :  4.954  20.676   1054
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 12.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.72 (0.26), residues: 948
  helix:  0.93 (0.26), residues: 367
  sheet: -0.64 (0.35), residues: 224
  loop : -1.84 (0.29), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  20 
 TYR   0.012   0.001   TYR R 263 
 PHE   0.017   0.001   PHE A 345 
 TRP   0.030   0.002   TRP B 339 
 HIS   0.005   0.001   HIS R 377 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 7806)
  covalent geometry    : angle       0.71023 (10578)
  SS BOND              : bond        0.00309 (    3)
  SS BOND              : angle       1.20948 (    6)
  hydrogen bonds       : bond        0.03960 (  398)
  hydrogen bonds       : angle       5.41639 ( 1149)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 284
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 GLN cc_start: 0.8104 (mt0) cc_final: 0.7874 (mt0)
REVERT: A   21 GLU cc_start: 0.6481 (tm-30) cc_final: 0.6208 (tm-30)
REVERT: A   29 GLN cc_start: 0.8649 (tm-30) cc_final: 0.8238 (tm-30)
REVERT: A   35 GLN cc_start: 0.8314 (pt0) cc_final: 0.7872 (pp30)
REVERT: A  389 ARG cc_start: 0.8096 (ttm110) cc_final: 0.7738 (ttm110)
REVERT: B   75 GLN cc_start: 0.8136 (tm-30) cc_final: 0.7776 (tm-30)
REVERT: B  127 LYS cc_start: 0.8235 (ptmm) cc_final: 0.7928 (ptmm)
REVERT: B  156 GLN cc_start: 0.8487 (pt0) cc_final: 0.8285 (pt0)
REVERT: B  171 ILE cc_start: 0.8145 (mm) cc_final: 0.7919 (mm)
REVERT: B  233 CYS cc_start: 0.8744 (t) cc_final: 0.8479 (t)
REVERT: B  339 TRP cc_start: 0.8137 (m-10) cc_final: 0.7577 (m-10)
REVERT: G   14 LYS cc_start: 0.8678 (mptt) cc_final: 0.8382 (mmtt)
REVERT: G   22 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7764 (tm-30)
REVERT: N    5 GLN cc_start: 0.7728 (tp-100) cc_final: 0.7274 (tm-30)
REVERT: N   78 THR cc_start: 0.8212 (p) cc_final: 0.7854 (p)
REVERT: R  187 MET cc_start: 0.7974 (mmm) cc_final: 0.7608 (tpt)
REVERT: R  197 ILE cc_start: 0.8885 (tt) cc_final: 0.8565 (tt)
REVERT: R  204 GLU cc_start: 0.7644 (tt0) cc_final: 0.7255 (mt-10)
REVERT: R  223 HIS cc_start: 0.8094 (t70) cc_final: 0.7859 (t70)
REVERT: R  262 TYR cc_start: 0.8392 (m-80) cc_final: 0.7957 (m-80)
REVERT: R  366 LYS cc_start: 0.7234 (tttt) cc_final: 0.6978 (tmtm)
REVERT: R  404 ARG cc_start: 0.8044 (ptm-80) cc_final: 0.7494 (ttp80)
  outliers start: 0
  outliers final: 0
  residues processed: 284
  average time/residue: 0.0994
  time to fit residues: 37.3088
Evaluate side-chains
  220 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 27 optimal weight:    8.9990
   chunk 66 optimal weight:    5.9990
   chunk 75 optimal weight:    0.2980
   chunk 21 optimal weight:    7.9990
   chunk 89 optimal weight:    1.9990
   chunk 71 optimal weight:    4.9990
   chunk 87 optimal weight:    5.9990
   chunk 59 optimal weight:    0.6980
   chunk 10 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   chunk 62 optimal weight:    8.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
** B  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
R 233 ASN
** R 381 HIS ** 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 = 0.3632 r_free = 0.3632 target = 0.125810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.102542 restraints weight = 14039.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.105314 restraints weight = 8037.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.107334 restraints weight = 5488.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.108721 restraints weight = 4179.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.109362 restraints weight = 3445.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.4109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7809  Z= 0.160
  Angle     :  0.683  10.142  10584  Z= 0.347
  Chirality :  0.044   0.180   1194
  Planarity :  0.005   0.049   1340
  Dihedral  :  4.840  19.942   1054
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.65 (0.26), residues: 948
  helix:  1.03 (0.25), residues: 366
  sheet: -0.73 (0.35), residues: 219
  loop : -1.73 (0.29), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG R 281 
 TYR   0.013   0.002   TYR A 360 
 PHE   0.026   0.002   PHE R 314 
 TRP   0.026   0.002   TRP R 413 
 HIS   0.005   0.001   HIS R 377 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 7806)
  covalent geometry    : angle       0.68284 (10578)
  SS BOND              : bond        0.00344 (    3)
  SS BOND              : angle       0.96529 (    6)
  hydrogen bonds       : bond        0.03887 (  398)
  hydrogen bonds       : angle       5.26490 ( 1149)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 267
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 GLN cc_start: 0.8328 (pt0) cc_final: 0.7701 (pp30)
REVERT: A  213 GLN cc_start: 0.8017 (mm110) cc_final: 0.7791 (tp40)
REVERT: A  218 ASN cc_start: 0.8295 (m-40) cc_final: 0.7948 (m110)
REVERT: A  389 ARG cc_start: 0.8189 (ttm110) cc_final: 0.7793 (ttm110)
REVERT: B   59 TYR cc_start: 0.8903 (m-80) cc_final: 0.8627 (m-80)
REVERT: B  127 LYS cc_start: 0.8271 (ptmm) cc_final: 0.7987 (ptmm)
REVERT: B  156 GLN cc_start: 0.8534 (pt0) cc_final: 0.8294 (pt0)
REVERT: B  171 ILE cc_start: 0.8108 (mm) cc_final: 0.7736 (mm)
REVERT: G   22 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7754 (tm-30)
REVERT: N    5 GLN cc_start: 0.7678 (tp-100) cc_final: 0.7327 (tm-30)
REVERT: N  103 PHE cc_start: 0.8169 (m-80) cc_final: 0.7907 (m-80)
REVERT: R  187 MET cc_start: 0.8149 (mmm) cc_final: 0.7884 (tpt)
REVERT: R  197 ILE cc_start: 0.8841 (tt) cc_final: 0.8546 (tt)
REVERT: R  204 GLU cc_start: 0.7578 (tt0) cc_final: 0.7170 (mt-10)
REVERT: R  223 HIS cc_start: 0.8020 (t70) cc_final: 0.7780 (t70)
REVERT: R  229 MET cc_start: 0.8915 (tpp) cc_final: 0.7925 (tpp)
REVERT: R  262 TYR cc_start: 0.8476 (m-80) cc_final: 0.8076 (m-80)
REVERT: R  366 LYS cc_start: 0.7237 (tttt) cc_final: 0.6913 (tttp)
REVERT: R  404 ARG cc_start: 0.7908 (ptm-80) cc_final: 0.7397 (ptm-80)
REVERT: R  406 TRP cc_start: 0.7848 (t60) cc_final: 0.7533 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 267
  average time/residue: 0.1006
  time to fit residues: 35.2976
Evaluate side-chains
  234 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 234
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 59 optimal weight:    7.9990
   chunk 17 optimal weight:    1.9990
   chunk 13 optimal weight:    7.9990
   chunk 92 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 83 optimal weight:    8.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
** B  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
** R 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 383 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.126298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.102734 restraints weight = 14048.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.105650 restraints weight = 7862.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.107777 restraints weight = 5310.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.109097 restraints weight = 3997.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.110085 restraints weight = 3301.498|
|-----------------------------------------------------------------------------|
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.4323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7809  Z= 0.151
  Angle     :  0.691  10.583  10584  Z= 0.348
  Chirality :  0.044   0.182   1194
  Planarity :  0.004   0.046   1340
  Dihedral  :  4.761  18.122   1054
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.61 (0.26), residues: 948
  helix:  1.11 (0.25), residues: 367
  sheet: -0.78 (0.35), residues: 218
  loop : -1.71 (0.29), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  20 
 TYR   0.015   0.001   TYR R 372 
 PHE   0.015   0.001   PHE A 345 
 TRP   0.019   0.002   TRP R 413 
 HIS   0.006   0.001   HIS R 377 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 7806)
  covalent geometry    : angle       0.69129 (10578)
  SS BOND              : bond        0.00281 (    3)
  SS BOND              : angle       0.87983 (    6)
  hydrogen bonds       : bond        0.03805 (  398)
  hydrogen bonds       : angle       5.14356 ( 1149)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 263
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 GLN cc_start: 0.8174 (pt0) cc_final: 0.7801 (pp30)
REVERT: A   36 VAL cc_start: 0.9263 (p) cc_final: 0.8866 (t)
REVERT: A  218 ASN cc_start: 0.8246 (m-40) cc_final: 0.7878 (m110)
REVERT: A  389 ARG cc_start: 0.8191 (ttm110) cc_final: 0.7849 (ttm110)
REVERT: B  127 LYS cc_start: 0.8301 (ptmm) cc_final: 0.8001 (ptmm)
REVERT: B  171 ILE cc_start: 0.8088 (mm) cc_final: 0.7740 (mm)
REVERT: B  233 CYS cc_start: 0.8778 (t) cc_final: 0.8489 (t)
REVERT: G   22 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7795 (tm-30)
REVERT: N    5 GLN cc_start: 0.7716 (tp-100) cc_final: 0.7347 (tm-30)
REVERT: N   70 ILE cc_start: 0.8997 (pt) cc_final: 0.8794 (pt)
REVERT: R  187 MET cc_start: 0.8189 (mmm) cc_final: 0.7771 (tpt)
REVERT: R  197 ILE cc_start: 0.8836 (tt) cc_final: 0.8512 (tt)
REVERT: R  204 GLU cc_start: 0.7595 (tt0) cc_final: 0.7165 (mt-10)
REVERT: R  223 HIS cc_start: 0.7956 (t70) cc_final: 0.7572 (t70)
REVERT: R  262 TYR cc_start: 0.8457 (m-80) cc_final: 0.8018 (m-80)
REVERT: R  348 LEU cc_start: 0.9070 (tt) cc_final: 0.8826 (pp)
REVERT: R  373 ASP cc_start: 0.7649 (m-30) cc_final: 0.7374 (p0)
REVERT: R  404 ARG cc_start: 0.7855 (ptm-80) cc_final: 0.7380 (ptm-80)
REVERT: R  406 TRP cc_start: 0.7809 (t60) cc_final: 0.7502 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 263
  average time/residue: 0.1000
  time to fit residues: 34.4787
Evaluate side-chains
  230 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   chunk 48 optimal weight:   10.0000
   chunk 92 optimal weight:    0.4980
   chunk 61 optimal weight:    6.9990
   chunk 23 optimal weight:    6.9990
   chunk 43 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 53 optimal weight:    0.0970
   chunk 35 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    1.0580

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

Flipped N/Q/H residues before XYZ refinement:
A 377 ASN
** A 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 110 ASN
B 340 ASN
R 227 GLN
** R 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 383 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.127363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.103465 restraints weight = 13883.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.106354 restraints weight = 7854.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.108442 restraints weight = 5338.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.109861 restraints weight = 4051.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.110770 restraints weight = 3339.674|
|-----------------------------------------------------------------------------|
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.4488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7809  Z= 0.133
  Angle     :  0.679  11.827  10584  Z= 0.339
  Chirality :  0.044   0.194   1194
  Planarity :  0.004   0.044   1340
  Dihedral  :  4.675  18.900   1054
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.51 (0.26), residues: 948
  helix:  1.19 (0.25), residues: 368
  sheet: -0.72 (0.36), residues: 207
  loop : -1.66 (0.30), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A  20 
 TYR   0.013   0.001   TYR R 372 
 PHE   0.011   0.001   PHE B 335 
 TRP   0.017   0.002   TRP R 413 
 HIS   0.006   0.001   HIS R 377 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 7806)
  covalent geometry    : angle       0.67928 (10578)
  SS BOND              : bond        0.00242 (    3)
  SS BOND              : angle       0.81714 (    6)
  hydrogen bonds       : bond        0.03627 (  398)
  hydrogen bonds       : angle       5.01599 ( 1149)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 268
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.8390 (mtmt) cc_final: 0.7841 (mttp)
REVERT: A   28 LYS cc_start: 0.8480 (tppt) cc_final: 0.8239 (tptp)
REVERT: A   29 GLN cc_start: 0.8702 (tp40) cc_final: 0.8400 (tp40)
REVERT: A   35 GLN cc_start: 0.8258 (pt0) cc_final: 0.7776 (pp30)
REVERT: A   36 VAL cc_start: 0.9166 (p) cc_final: 0.8691 (p)
REVERT: A  342 ARG cc_start: 0.7377 (ttt180) cc_final: 0.7096 (ptm-80)
REVERT: A  389 ARG cc_start: 0.8142 (ttm110) cc_final: 0.7807 (ttm110)
REVERT: B  127 LYS cc_start: 0.8295 (ptmm) cc_final: 0.7995 (ptmm)
REVERT: B  171 ILE cc_start: 0.8115 (mm) cc_final: 0.7727 (mm)
REVERT: G   22 GLU cc_start: 0.8286 (tm-30) cc_final: 0.8067 (tm-30)
REVERT: N    5 GLN cc_start: 0.7645 (tp-100) cc_final: 0.7359 (tm-30)
REVERT: N   31 ASN cc_start: 0.8988 (m110) cc_final: 0.8782 (m-40)
REVERT: R  187 MET cc_start: 0.8227 (mmm) cc_final: 0.7706 (tpt)
REVERT: R  197 ILE cc_start: 0.8794 (tt) cc_final: 0.8429 (tt)
REVERT: R  204 GLU cc_start: 0.7591 (tt0) cc_final: 0.7158 (mt-10)
REVERT: R  223 HIS cc_start: 0.8075 (t70) cc_final: 0.7684 (t70)
REVERT: R  262 TYR cc_start: 0.8353 (m-80) cc_final: 0.8001 (m-80)
REVERT: R  340 LYS cc_start: 0.8257 (pttt) cc_final: 0.7637 (pptt)
REVERT: R  348 LEU cc_start: 0.9047 (tt) cc_final: 0.8832 (pp)
REVERT: R  373 ASP cc_start: 0.7662 (m-30) cc_final: 0.7394 (p0)
REVERT: R  404 ARG cc_start: 0.7794 (ptm-80) cc_final: 0.7386 (ptm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 268
  average time/residue: 0.0949
  time to fit residues: 33.7225
Evaluate side-chains
  232 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 232
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 67 optimal weight:    6.9990
   chunk 91 optimal weight:    7.9990
   chunk 85 optimal weight:    0.7980
   chunk 75 optimal weight:    0.8980
   chunk 4 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 89 optimal weight:    0.0770
   chunk 31 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.9542

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 213 GLN
A 218 ASN
B  13 GLN
** B  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
R 227 GLN
** R 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 383 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.127569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.104152 restraints weight = 13869.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.106974 restraints weight = 7907.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.108850 restraints weight = 5401.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.110275 restraints weight = 4155.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.111316 restraints weight = 3459.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.4649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7809  Z= 0.131
  Angle     :  0.675  12.321  10584  Z= 0.337
  Chirality :  0.044   0.197   1194
  Planarity :  0.004   0.044   1340
  Dihedral  :  4.569  19.386   1054
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.87 %
    Favored  : 99.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.42 (0.26), residues: 948
  helix:  1.36 (0.25), residues: 364
  sheet: -0.60 (0.37), residues: 195
  loop : -1.72 (0.29), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  20 
 TYR   0.014   0.001   TYR R 263 
 PHE   0.010   0.001   PHE R 161 
 TRP   0.029   0.002   TRP R 413 
 HIS   0.006   0.001   HIS R 381 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 7806)
  covalent geometry    : angle       0.67514 (10578)
  SS BOND              : bond        0.00231 (    3)
  SS BOND              : angle       0.81159 (    6)
  hydrogen bonds       : bond        0.03543 (  398)
  hydrogen bonds       : angle       4.89849 ( 1149)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 271
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.8343 (mtmt) cc_final: 0.7858 (mttp)
REVERT: A   28 LYS cc_start: 0.8556 (tppt) cc_final: 0.8309 (tppt)
REVERT: A   35 GLN cc_start: 0.8310 (pt0) cc_final: 0.7754 (pp30)
REVERT: A   36 VAL cc_start: 0.9167 (p) cc_final: 0.8591 (p)
REVERT: A  271 ASN cc_start: 0.7568 (t0) cc_final: 0.7356 (t0)
REVERT: A  342 ARG cc_start: 0.7396 (ttt180) cc_final: 0.7122 (ptm-80)
REVERT: A  357 HIS cc_start: 0.7712 (p-80) cc_final: 0.7387 (p-80)
REVERT: A  389 ARG cc_start: 0.8107 (ttm110) cc_final: 0.7835 (ttm110)
REVERT: B   15 LYS cc_start: 0.8534 (pptt) cc_final: 0.8155 (ptmt)
REVERT: B   55 LEU cc_start: 0.9224 (mp) cc_final: 0.8995 (mt)
REVERT: B  127 LYS cc_start: 0.8283 (ptmm) cc_final: 0.8003 (ptmm)
REVERT: B  171 ILE cc_start: 0.8107 (mm) cc_final: 0.7745 (mm)
REVERT: G   22 GLU cc_start: 0.8423 (tm-30) cc_final: 0.8194 (tm-30)
REVERT: N    5 GLN cc_start: 0.7664 (tp-100) cc_final: 0.7384 (tm-30)
REVERT: R  187 MET cc_start: 0.8298 (mmm) cc_final: 0.7626 (tpt)
REVERT: R  204 GLU cc_start: 0.7434 (tt0) cc_final: 0.6957 (mt-10)
REVERT: R  223 HIS cc_start: 0.8072 (t70) cc_final: 0.7656 (t70)
REVERT: R  229 MET cc_start: 0.8848 (tpp) cc_final: 0.7774 (tpp)
REVERT: R  262 TYR cc_start: 0.8276 (m-80) cc_final: 0.7916 (m-80)
REVERT: R  279 ILE cc_start: 0.7586 (mt) cc_final: 0.7135 (pt)
REVERT: R  340 LYS cc_start: 0.8216 (pttt) cc_final: 0.7826 (pptt)
REVERT: R  373 ASP cc_start: 0.7603 (m-30) cc_final: 0.7113 (p0)
REVERT: R  404 ARG cc_start: 0.7666 (ptm-80) cc_final: 0.7267 (ptm-80)
REVERT: R  406 TRP cc_start: 0.7957 (t60) cc_final: 0.7241 (t60)
  outliers start: 1
  outliers final: 0
  residues processed: 271
  average time/residue: 0.0950
  time to fit residues: 34.2383
Evaluate side-chains
  233 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 233
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 37 optimal weight:    0.6980
   chunk 29 optimal weight:    0.7980
   chunk 53 optimal weight:    7.9990
   chunk 42 optimal weight:    1.9990
   chunk 81 optimal weight:    6.9990
   chunk 20 optimal weight:   20.0000
   chunk 71 optimal weight:    0.9990
   chunk 28 optimal weight:    5.9990
   chunk 70 optimal weight:    6.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 377 ASN
** B  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
N   3 GLN
R 227 GLN
** R 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 383 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.126324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.102760 restraints weight = 13946.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.105554 restraints weight = 7866.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.107518 restraints weight = 5332.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.109022 restraints weight = 4090.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.109892 restraints weight = 3357.897|
|-----------------------------------------------------------------------------|
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.4758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   7809  Z= 0.154
  Angle     :  0.699  11.942  10584  Z= 0.350
  Chirality :  0.044   0.194   1194
  Planarity :  0.004   0.045   1340
  Dihedral  :  4.610  18.948   1054
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.40 (0.26), residues: 948
  helix:  1.32 (0.25), residues: 368
  sheet: -0.57 (0.37), residues: 201
  loop : -1.69 (0.30), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  20 
 TYR   0.015   0.002   TYR R 263 
 PHE   0.013   0.001   PHE B 234 
 TRP   0.025   0.002   TRP R 413 
 HIS   0.006   0.001   HIS R 381 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 7806)
  covalent geometry    : angle       0.69873 (10578)
  SS BOND              : bond        0.00302 (    3)
  SS BOND              : angle       0.81328 (    6)
  hydrogen bonds       : bond        0.03629 (  398)
  hydrogen bonds       : angle       4.93714 ( 1149)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 264
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 GLN cc_start: 0.8368 (pt0) cc_final: 0.7786 (pp30)
REVERT: A   36 VAL cc_start: 0.9167 (p) cc_final: 0.8612 (p)
REVERT: A  342 ARG cc_start: 0.7382 (ttt180) cc_final: 0.7131 (ptm-80)
REVERT: A  389 ARG cc_start: 0.8159 (ttm110) cc_final: 0.7875 (ttm110)
REVERT: B   15 LYS cc_start: 0.8500 (pptt) cc_final: 0.8109 (ptmt)
REVERT: B   55 LEU cc_start: 0.9216 (mp) cc_final: 0.8912 (mt)
REVERT: B  127 LYS cc_start: 0.8288 (ptmm) cc_final: 0.8007 (ptmm)
REVERT: B  171 ILE cc_start: 0.8143 (mm) cc_final: 0.7778 (mm)
REVERT: N   70 ILE cc_start: 0.8949 (pt) cc_final: 0.8737 (pt)
REVERT: R  187 MET cc_start: 0.8258 (mmm) cc_final: 0.7552 (tpt)
REVERT: R  204 GLU cc_start: 0.7568 (tt0) cc_final: 0.6555 (mm-30)
REVERT: R  223 HIS cc_start: 0.8113 (t70) cc_final: 0.7662 (t70)
REVERT: R  229 MET cc_start: 0.8871 (tpp) cc_final: 0.7848 (tpp)
REVERT: R  262 TYR cc_start: 0.8330 (m-80) cc_final: 0.8037 (m-80)
REVERT: R  279 ILE cc_start: 0.7679 (mt) cc_final: 0.7244 (pt)
REVERT: R  340 LYS cc_start: 0.8226 (pttt) cc_final: 0.7854 (pptt)
REVERT: R  373 ASP cc_start: 0.7613 (m-30) cc_final: 0.7352 (p0)
REVERT: R  404 ARG cc_start: 0.7686 (ptm-80) cc_final: 0.7297 (ptm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 264
  average time/residue: 0.0928
  time to fit residues: 32.5252
Evaluate side-chains
  226 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 226
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 75 optimal weight:    6.9990
   chunk 63 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9980
   chunk 38 optimal weight:    0.7980
   chunk 93 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 5 optimal weight:    6.9990
   chunk 3 optimal weight:    0.0270
   overall best weight:    1.1240

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 377 ASN
B  13 GLN
** B  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
R 223 HIS
** R 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 383 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.127059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.103496 restraints weight = 13864.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.106429 restraints weight = 7804.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.108477 restraints weight = 5272.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.109935 restraints weight = 4004.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.110535 restraints weight = 3294.407|
|-----------------------------------------------------------------------------|
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.4849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7809  Z= 0.140
  Angle     :  0.705  12.475  10584  Z= 0.352
  Chirality :  0.044   0.194   1194
  Planarity :  0.004   0.046   1340
  Dihedral  :  4.546  18.683   1054
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.62 %
    Favored  : 99.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.41 (0.26), residues: 948
  helix:  1.31 (0.25), residues: 370
  sheet: -0.57 (0.37), residues: 201
  loop : -1.71 (0.30), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  20 
 TYR   0.014   0.001   TYR R 263 
 PHE   0.010   0.001   PHE R 161 
 TRP   0.025   0.002   TRP R 413 
 HIS   0.016   0.002   HIS R 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 7806)
  covalent geometry    : angle       0.70488 (10578)
  SS BOND              : bond        0.00257 (    3)
  SS BOND              : angle       0.81658 (    6)
  hydrogen bonds       : bond        0.03584 (  398)
  hydrogen bonds       : angle       4.91146 ( 1149)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 262
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.8310 (mttp) cc_final: 0.7931 (mttp)
REVERT: A   28 LYS cc_start: 0.8589 (tppt) cc_final: 0.8180 (tppt)
REVERT: A   35 GLN cc_start: 0.8362 (pt0) cc_final: 0.7811 (pp30)
REVERT: A   36 VAL cc_start: 0.9145 (p) cc_final: 0.8525 (p)
REVERT: A  342 ARG cc_start: 0.7403 (ttt180) cc_final: 0.7068 (ptm-80)
REVERT: A  357 HIS cc_start: 0.7559 (p-80) cc_final: 0.6940 (p-80)
REVERT: A  389 ARG cc_start: 0.8138 (ttm110) cc_final: 0.7855 (ttm110)
REVERT: B   15 LYS cc_start: 0.8469 (pptt) cc_final: 0.8102 (ptpt)
REVERT: B   55 LEU cc_start: 0.9207 (mp) cc_final: 0.8923 (mt)
REVERT: B  127 LYS cc_start: 0.8300 (ptmm) cc_final: 0.8016 (ptmm)
REVERT: B  171 ILE cc_start: 0.8091 (mm) cc_final: 0.7766 (mm)
REVERT: N   70 ILE cc_start: 0.8944 (pt) cc_final: 0.8717 (pt)
REVERT: R  187 MET cc_start: 0.8285 (mmm) cc_final: 0.7594 (tpt)
REVERT: R  204 GLU cc_start: 0.7532 (tt0) cc_final: 0.6488 (mm-30)
REVERT: R  229 MET cc_start: 0.8909 (tpp) cc_final: 0.7935 (tpp)
REVERT: R  262 TYR cc_start: 0.8357 (m-80) cc_final: 0.8054 (m-80)
REVERT: R  279 ILE cc_start: 0.7722 (mt) cc_final: 0.7302 (pt)
REVERT: R  340 LYS cc_start: 0.8156 (pttt) cc_final: 0.7786 (pptt)
REVERT: R  373 ASP cc_start: 0.7628 (m-30) cc_final: 0.7408 (p0)
REVERT: R  399 GLN cc_start: 0.7917 (pt0) cc_final: 0.7699 (pt0)
  outliers start: 1
  outliers final: 1
  residues processed: 262
  average time/residue: 0.0953
  time to fit residues: 33.0681
Evaluate side-chains
  231 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 230
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 43 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 84 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   chunk 12 optimal weight:    9.9990
   chunk 63 optimal weight:    0.0570
   chunk 85 optimal weight:    6.9990
   overall best weight:    1.7304

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
N  13 GLN
** R 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 383 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.125522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.101880 restraints weight = 13984.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.104638 restraints weight = 7989.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.106676 restraints weight = 5446.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.108094 restraints weight = 4161.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.108888 restraints weight = 3435.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.4892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   7809  Z= 0.166
  Angle     :  0.719  11.202  10584  Z= 0.361
  Chirality :  0.045   0.183   1194
  Planarity :  0.004   0.046   1340
  Dihedral  :  4.642  19.561   1054
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.39 (0.27), residues: 948
  helix:  1.37 (0.25), residues: 368
  sheet: -0.62 (0.37), residues: 201
  loop : -1.70 (0.30), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  20 
 TYR   0.016   0.002   TYR A 358 
 PHE   0.013   0.001   PHE A 345 
 TRP   0.024   0.002   TRP R 413 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 7806)
  covalent geometry    : angle       0.71897 (10578)
  SS BOND              : bond        0.00332 (    3)
  SS BOND              : angle       0.88092 (    6)
  hydrogen bonds       : bond        0.03639 (  398)
  hydrogen bonds       : angle       4.96384 ( 1149)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1494.83 seconds
wall clock time: 26 minutes 32.74 seconds (1592.74 seconds total)