Starting phenix.real_space_refine
on Fri Feb 14 03:25:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5fn5_3240/02_2025/5fn5_3240.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5fn5_3240/02_2025/5fn5_3240.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5fn5_3240/02_2025/5fn5_3240.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5fn5_3240/02_2025/5fn5_3240.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5fn5_3240/02_2025/5fn5_3240.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5fn5_3240/02_2025/5fn5_3240.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    6313      2.51       5
     N    1572      2.21       5
     O    1724      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9645
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5222
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 665, 5222
          Classifications: {'peptide': 665}
          Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 627}
    Chain: "B"
      Number of atoms: 1735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1735
          Classifications: {'peptide': 223}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 215}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 43
          Unresolved non-hydrogen angles: 55
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 30
    Chain: "C"
      Number of atoms: 1868
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 243, 1868
          Classifications: {'peptide': 243}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 233}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "D"
      Number of atoms: 820
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 820
          Classifications: {'peptide': 96}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 91}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
  Time building chain proxies: 5.45, per 1000 atoms: 0.57
  Number of scatterers: 9645
  At special positions: 0
  Unit cell: (93.8, 142.8, 96.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      36     16.00
     O    1724      8.00
     N    1572      7.00
     C    6313      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  50 " - pdb=" SG  CYS A  62 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 140 " - pdb=" SG  CYS A 159 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 195 " - pdb=" SG  CYS A 213 " distance=2.07
    Simple disulfide: pdb=" SG  CYS A 230 " - pdb=" SG  CYS A 248 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 586 " - pdb=" SG  CYS A 620 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.62
  Conformation dependent library (CDL) restraints added in 984.0 milliseconds
  

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2308

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 7 sheets defined
      59.1% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'A' and resid 34 through 41
      removed outlier: 3.842A  pdb=" N   ARG A  38 " --> pdb=" O   ASN A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 88
    Processing helix  chain 'A' and resid 105 through 113
    Processing helix  chain 'A' and resid 142 through 146
      removed outlier: 3.892A  pdb=" N   GLY A 146 " --> pdb=" O   ASP A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 200
      removed outlier: 4.198A  pdb=" N   THR A 189 " --> pdb=" O   ASP A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 240
    Processing helix  chain 'A' and resid 298 through 314
    Processing helix  chain 'A' and resid 337 through 350
    Processing helix  chain 'A' and resid 381 through 387
    Processing helix  chain 'A' and resid 387 through 407
      removed outlier: 3.666A  pdb=" N   GLY A 407 " --> pdb=" O   LYS A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 431
      removed outlier: 4.025A  pdb=" N   ARG A 429 " --> pdb=" O   SER A 425 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 434
      No H-bonds generated for 'chain 'A' and resid 432 through 434'
    Processing helix  chain 'A' and resid 459 through 464
    Processing helix  chain 'A' and resid 474 through 479
      removed outlier: 4.065A  pdb=" N   ASN A 478 " --> pdb=" O   GLU A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 504
      removed outlier: 3.570A  pdb=" N   GLY A 504 " --> pdb=" O   GLU A 500 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 514 through 527
      removed outlier: 3.733A  pdb=" N   VAL A 518 " --> pdb=" O   ASP A 514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 531 through 537
    Processing helix  chain 'A' and resid 541 through 546
    Processing helix  chain 'A' and resid 561 through 575
      removed outlier: 3.541A  pdb=" N   VAL A 566 " --> pdb=" O   ASN A 562 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 582 through 588
    Processing helix  chain 'A' and resid 633 through 638
    Processing helix  chain 'A' and resid 665 through 698
      removed outlier: 5.173A  pdb=" N   ASP A 695 " --> pdb=" O   ASN A 691 " (cutoff:3.500A)
      removed outlier: 5.911A  pdb=" N   VAL A 696 " --> pdb=" O   ALA A 692 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 102
      Proline residue:  B  88  - end of helix
      removed outlier: 3.509A  pdb=" N   LEU B  91 " --> pdb=" O   VAL B  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 190
      removed outlier: 3.676A  pdb=" N   PHE B 179 " --> pdb=" O   PHE B 175 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ILE B 180 " --> pdb=" O   PHE B 176 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   THR B 188 " --> pdb=" O   GLU B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 195 through 214
    Processing helix  chain 'B' and resid 218 through 240
    Processing helix  chain 'B' and resid 244 through 263
    Processing helix  chain 'B' and resid 382 through 398
    Processing helix  chain 'B' and resid 403 through 429
      removed outlier: 3.699A  pdb=" N   THR B 421 " --> pdb=" O   GLY B 417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 435 through 464
      removed outlier: 3.675A  pdb=" N   VAL B 444 " --> pdb=" O   THR B 440 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   PHE B 445 " --> pdb=" O   PHE B 441 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   GLN B 454 " --> pdb=" O   ASP B 450 " (cutoff:3.500A)
      Proline residue:  B 455  - end of helix
    Processing helix  chain 'C' and resid 2 through 24
      Proline residue:  C  16  - end of helix
    Processing helix  chain 'C' and resid 28 through 60
      removed outlier: 3.557A  pdb=" N   VAL C  32 " --> pdb=" O   ASP C  28 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 67 through 102
    Processing helix  chain 'C' and resid 103 through 105
      No H-bonds generated for 'chain 'C' and resid 103 through 105'
    Processing helix  chain 'C' and resid 114 through 142
      removed outlier: 3.654A  pdb=" N   SER C 129 " --> pdb=" O   PHE C 125 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   ASN C 136 " --> pdb=" O   PHE C 132 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   ILE C 137 " --> pdb=" O   SER C 133 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   ALA C 139 " --> pdb=" O   ILE C 135 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 155 through 185
      removed outlier: 3.510A  pdb=" N   PHE C 179 " --> pdb=" O   GLY C 175 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   ASP C 180 " --> pdb=" O   VAL C 176 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 186 through 206
      removed outlier: 3.939A  pdb=" N   LEU C 190 " --> pdb=" O   ARG C 186 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 213 through 233
      removed outlier: 3.759A  pdb=" N   ILE C 217 " --> pdb=" O   SER C 213 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 235 through 243
      removed outlier: 3.590A  pdb=" N   LEU C 243 " --> pdb=" O   ILE C 239 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 8 through 20
      removed outlier: 3.801A  pdb=" N   ASN D  13 " --> pdb=" O   GLU D   9 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 26 through 42
      removed outlier: 3.782A  pdb=" N   TRP D  30 " --> pdb=" O   LEU D  26 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   TRP D  36 " --> pdb=" O   VAL D  32 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 49 through 54
    Processing helix  chain 'D' and resid 55 through 82
    Processing helix  chain 'D' and resid 86 through 92
    Processing sheet with id=AA, first strand: chain 'A' and resid 42 through 43
      removed outlier: 6.559A  pdb=" N   CYS A 213 " --> pdb=" O   ILE A  73 " (cutoff:3.500A)
    Processing sheet with id=AB, first strand: chain 'A' and resid 59 through 60
    Processing sheet with id=AC, first strand: chain 'A' and resid 413 through 414
      removed outlier: 3.543A  pdb=" N   VAL A 440 " --> pdb=" O   HIS A 379 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   SER A 437 " --> pdb=" O   PHE A 362 " (cutoff:3.500A)
    Processing sheet with id=AD, first strand: chain 'A' and resid 413 through 414
      removed outlier: 3.543A  pdb=" N   VAL A 440 " --> pdb=" O   HIS A 379 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   SER A 361 " --> pdb=" O   VAL A 275 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   TRP A 257 " --> pdb=" O   ARG A 626 " (cutoff:3.500A)
    Processing sheet with id=AE, first strand: chain 'A' and resid 437 through 438
      removed outlier: 6.800A  pdb=" N   SER A 437 " --> pdb=" O   PHE A 362 " (cutoff:3.500A)
    Processing sheet with id=AF, first strand: chain 'A' and resid 603 through 604
    Processing sheet with id=BA, first strand: chain 'B' and resid 193 through 194
      removed outlier: 6.969A  pdb=" N   VAL B 193 " --> pdb=" O   PHE D  94 " (cutoff:3.500A)

    572 hydrogen bonds defined for protein.
    1671 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.09

  Time building geometry restraints manager: 3.02 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1599
        1.32 -     1.45: 2853
        1.45 -     1.58: 5376
        1.58 -     1.71: 12
        1.71 -     1.83: 54
  Bond restraints: 9894
  Sorted by residual:
  bond pdb=" CA  SER B 401 "
       pdb=" C   SER B 401 "
    ideal  model  delta    sigma   weight residual
    1.523  1.608 -0.084 1.34e-02 5.57e+03 3.97e+01
  bond pdb=" N   LEU C 243 "
       pdb=" CA  LEU C 243 "
    ideal  model  delta    sigma   weight residual
    1.457  1.528 -0.070 1.29e-02 6.01e+03 2.98e+01
  bond pdb=" CA  VAL A 579 "
       pdb=" C   VAL A 579 "
    ideal  model  delta    sigma   weight residual
    1.520  1.578 -0.058 1.07e-02 8.73e+03 2.95e+01
  bond pdb=" CA  LEU B 452 "
       pdb=" C   LEU B 452 "
    ideal  model  delta    sigma   weight residual
    1.525  1.476  0.050 1.02e-02 9.61e+03 2.37e+01
  bond pdb=" CA  LEU C 243 "
       pdb=" C   LEU C 243 "
    ideal  model  delta    sigma   weight residual
    1.523  1.582 -0.059 1.34e-02 5.57e+03 1.95e+01
  ... (remaining 9889 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.57: 11297
        2.57 -     5.15: 1993
        5.15 -     7.72: 166
        7.72 -    10.30: 23
       10.30 -    12.87: 9
  Bond angle restraints: 13488
  Sorted by residual:
  angle pdb=" N   VAL C 120 "
        pdb=" CA  VAL C 120 "
        pdb=" CB  VAL C 120 "
      ideal   model   delta    sigma   weight residual
     110.55  119.51   -8.96 1.17e+00 7.31e-01 5.87e+01
  angle pdb=" N   GLY A 547 "
        pdb=" CA  GLY A 547 "
        pdb=" C   GLY A 547 "
      ideal   model   delta    sigma   weight residual
     112.57  102.37   10.20 1.37e+00 5.33e-01 5.54e+01
  angle pdb=" N   ALA B 400 "
        pdb=" CA  ALA B 400 "
        pdb=" C   ALA B 400 "
      ideal   model   delta    sigma   weight residual
     109.40  121.49  -12.09 1.63e+00 3.76e-01 5.50e+01
  angle pdb=" CA  PHE C  88 "
        pdb=" C   PHE C  88 "
        pdb=" N   ALA C  89 "
      ideal   model   delta    sigma   weight residual
     117.07  108.95    8.12 1.14e+00 7.69e-01 5.07e+01
  angle pdb=" C   ILE B 387 "
        pdb=" CA  ILE B 387 "
        pdb=" CB  ILE B 387 "
      ideal   model   delta    sigma   weight residual
     111.97  102.87    9.10 1.28e+00 6.10e-01 5.06e+01
  ... (remaining 13483 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.40: 4792
       17.40 -    34.79: 691
       34.79 -    52.19: 221
       52.19 -    69.59: 57
       69.59 -    86.99: 10
  Dihedral angle restraints: 5771
    sinusoidal: 2196
      harmonic: 3575
  Sorted by residual:
  dihedral pdb=" CA  ALA B 400 "
           pdb=" C   ALA B 400 "
           pdb=" N   SER B 401 "
           pdb=" CA  SER B 401 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -128.06  -51.94     0      5.00e+00 4.00e-02 1.08e+02
  dihedral pdb=" CB  CYS A 230 "
           pdb=" SG  CYS A 230 "
           pdb=" SG  CYS A 248 "
           pdb=" CB  CYS A 248 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  179.99  -86.99     1      1.00e+01 1.00e-02 9.10e+01
  dihedral pdb=" CA  TYR B 106 "
           pdb=" C   TYR B 106 "
           pdb=" N   THR B 107 "
           pdb=" CA  THR B 107 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  132.58   47.42     0      5.00e+00 4.00e-02 8.99e+01
  ... (remaining 5768 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.151: 1341
       0.151 -    0.301: 185
       0.301 -    0.452: 26
       0.452 -    0.602: 6
       0.602 -    0.753: 2
  Chirality restraints: 1560
  Sorted by residual:
  chirality pdb=" CA  PHE A 218 "
            pdb=" N   PHE A 218 "
            pdb=" C   PHE A 218 "
            pdb=" CB  PHE A 218 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.76    0.75 2.00e-01 2.50e+01 1.42e+01
  chirality pdb=" CA  PHE A 302 "
            pdb=" N   PHE A 302 "
            pdb=" C   PHE A 302 "
            pdb=" CB  PHE A 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.78    0.73 2.00e-01 2.50e+01 1.33e+01
  chirality pdb=" CA  TYR B 225 "
            pdb=" N   TYR B 225 "
            pdb=" C   TYR B 225 "
            pdb=" CB  TYR B 225 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.93    0.58 2.00e-01 2.50e+01 8.45e+00
  ... (remaining 1557 not shown)

  Planarity restraints: 1680
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 559 "    0.072 5.00e-02 4.00e+02   1.10e-01 1.92e+01
        pdb=" N   PRO A 560 "   -0.190 5.00e-02 4.00e+02
        pdb=" CA  PRO A 560 "    0.062 5.00e-02 4.00e+02
        pdb=" CD  PRO A 560 "    0.056 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B  87 "    0.064 5.00e-02 4.00e+02   9.62e-02 1.48e+01
        pdb=" N   PRO B  88 "   -0.166 5.00e-02 4.00e+02
        pdb=" CA  PRO B  88 "    0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO B  88 "    0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 388 "    0.038 2.00e-02 2.50e+03   2.64e-02 1.22e+01
        pdb=" CG  PHE B 388 "   -0.056 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 388 "    0.000 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 388 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 388 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 388 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 388 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1677 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 132
        2.64 -     3.20: 9550
        3.20 -     3.77: 16000
        3.77 -     4.33: 20541
        4.33 -     4.90: 33144
  Nonbonded interactions: 79367
  Sorted by model distance:
  nonbonded pdb=" O   ILE C  34 "
            pdb=" OH  TYR C  90 "
     model   vdw
     2.074 3.040
  nonbonded pdb=" O   ALA B 396 "
            pdb=" OG1 THR B 399 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" O   LEU A 397 "
            pdb=" OG1 THR A 400 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" O   LEU C  35 "
            pdb=" OG  SER C 124 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" O   ALA C  76 "
            pdb=" OG  SER C  79 "
     model   vdw
     2.280 3.040
  ... (remaining 79362 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.250
  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:          0.320
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     23.980
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6489
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.012   0.095   9894  Z= 0.780
  Angle     :  1.850  12.870  13488  Z= 1.292
  Chirality :  0.113   0.753   1560
  Planarity :  0.008   0.110   1680
  Dihedral  : 18.823  81.957   3448
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 13.59
  Ramachandran Plot:
    Outliers :  4.30 %
    Allowed  : 11.41 %
    Favored  : 84.28 %
  Rotamer:
    Outliers : 14.00 %
    Allowed  : 16.49 %
    Favored  : 69.51 %
  Cbeta Deviations :  2.43 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 1.85 %
    Twisted General : 1.29 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.91 (0.22), residues: 1209
  helix:  1.07 (0.16), residues: 660
  sheet: -3.39 (0.45), residues: 100
  loop : -4.58 (0.22), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.004   TRP D  36 
 HIS   0.013   0.003   HIS A  74 
 PHE   0.059   0.005   PHE A 302 
 TYR   0.042   0.004   TYR B 225 
 ARG   0.008   0.001   ARG A 657 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  386 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 146
    poor density    : 240
  time to evaluate  : 1.063 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 SER cc_start: 0.6710 (OUTLIER) cc_final: 0.6345 (p)
REVERT: A   95 MET cc_start: 0.9170 (mmt) cc_final: 0.8700 (mmm)
REVERT: A  129 SER cc_start: 0.7373 (OUTLIER) cc_final: 0.6535 (t)
REVERT: A  237 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8194 (tp-100)
REVERT: A  333 GLU cc_start: 0.9323 (OUTLIER) cc_final: 0.8792 (mp0)
REVERT: A  378 MET cc_start: 0.9135 (mpt) cc_final: 0.8745 (mpp)
REVERT: A  425 SER cc_start: 0.8302 (OUTLIER) cc_final: 0.7908 (t)
REVERT: A  426 SER cc_start: 0.9586 (t) cc_final: 0.8770 (p)
REVERT: A  430 PHE cc_start: 0.9607 (m-80) cc_final: 0.9003 (m-80)
REVERT: A  512 GLN cc_start: 0.9340 (OUTLIER) cc_final: 0.8960 (pp30)
REVERT: A  522 LEU cc_start: 0.9666 (OUTLIER) cc_final: 0.9433 (mt)
REVERT: A  555 ILE cc_start: 0.7981 (mt) cc_final: 0.6549 (mt)
REVERT: A  574 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8803 (mt)
REVERT: A  624 THR cc_start: 0.7194 (OUTLIER) cc_final: 0.6823 (m)
REVERT: A  644 GLU cc_start: 0.9115 (OUTLIER) cc_final: 0.8895 (pp20)
REVERT: A  655 ASP cc_start: 0.8547 (m-30) cc_final: 0.8202 (p0)
REVERT: B   80 LYS cc_start: 0.9357 (tttt) cc_final: 0.9022 (mttm)
REVERT: B  105 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8396 (t80)
REVERT: B  184 GLU cc_start: 0.9375 (OUTLIER) cc_final: 0.9130 (mm-30)
REVERT: B  194 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8142 (p0)
REVERT: B  195 TYR cc_start: 0.8934 (OUTLIER) cc_final: 0.8656 (m-80)
REVERT: B  386 PHE cc_start: 0.8150 (t80) cc_final: 0.7820 (t80)
REVERT: B  405 ASN cc_start: 0.8830 (t0) cc_final: 0.8514 (t0)
REVERT: B  438 SER cc_start: 0.8016 (OUTLIER) cc_final: 0.7749 (p)
REVERT: C    9 CYS cc_start: 0.8973 (m) cc_final: 0.8604 (p)
REVERT: C   83 GLN cc_start: 0.9499 (mt0) cc_final: 0.9275 (mp10)
REVERT: C   84 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8619 (mm-30)
REVERT: C  132 PHE cc_start: 0.9522 (m-10) cc_final: 0.9304 (m-10)
REVERT: C  136 ASN cc_start: 0.9112 (m-40) cc_final: 0.8562 (p0)
REVERT: D    5 ARG cc_start: 0.8240 (mtm180) cc_final: 0.8029 (ptt90)
REVERT: D   28 PHE cc_start: 0.9231 (t80) cc_final: 0.8868 (t80)
REVERT: D   84 ARG cc_start: 0.9253 (mtt180) cc_final: 0.9022 (mpt-90)
REVERT: D   96 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7658 (mm)
  outliers start: 146
  outliers final: 47
  residues processed: 346
  average time/residue: 0.2145
  time to fit residues: 103.0929
Evaluate side-chains
  223 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 160
  time to evaluate  : 1.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 102 optimal weight:    7.9990
   chunk 91 optimal weight:    5.9990
   chunk 50 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 94 optimal weight:    6.9990
   chunk 36 optimal weight:    3.9990
   chunk 57 optimal weight:    8.9990
   chunk 70 optimal weight:    0.4980
   chunk 109 optimal weight:    5.9990
   overall best weight:    2.2988

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

Flipped N/Q/H residues before XYZ refinement:
A 142 ASN
A 237 GLN
** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 516 GLN
A 535 GLN
** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 223 GLN
C 171 HIS
** D   8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.053476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.045783 restraints weight = 68223.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.046861 restraints weight = 44590.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.047689 restraints weight = 32375.994|
|-----------------------------------------------------------------------------|
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.4183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   9894  Z= 0.287
  Angle     :  0.873  11.272  13488  Z= 0.454
  Chirality :  0.048   0.197   1560
  Planarity :  0.006   0.090   1680
  Dihedral  :  7.200  35.800   1319
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 17.12
  Ramachandran Plot:
    Outliers :  1.08 %
    Allowed  :  8.35 %
    Favored  : 90.57 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  3.93 %
    Favored  : 95.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 3.70 %
    Twisted General : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.25), residues: 1209
  helix:  1.87 (0.20), residues: 692
  sheet: -2.88 (0.44), residues: 109
  loop : -3.92 (0.25), residues: 408

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

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 225
  time to evaluate  : 1.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  251 LEU cc_start: 0.9405 (mt) cc_final: 0.9053 (mt)
REVERT: A  305 GLN cc_start: 0.9463 (tp-100) cc_final: 0.9132 (tt0)
REVERT: A  349 LYS cc_start: 0.9518 (mmtt) cc_final: 0.9168 (mmtp)
REVERT: A  430 PHE cc_start: 0.8992 (m-80) cc_final: 0.8748 (m-80)
REVERT: A  457 TYR cc_start: 0.8353 (m-80) cc_final: 0.7872 (m-80)
REVERT: A  538 LEU cc_start: 0.9345 (mt) cc_final: 0.9028 (mt)
REVERT: A  553 HIS cc_start: 0.9118 (m-70) cc_final: 0.8872 (m90)
REVERT: A  655 ASP cc_start: 0.8769 (m-30) cc_final: 0.8448 (p0)
REVERT: A  657 ARG cc_start: 0.9078 (ptt-90) cc_final: 0.8654 (ptt90)
REVERT: A  670 LEU cc_start: 0.9641 (mt) cc_final: 0.9413 (mt)
REVERT: A  673 LEU cc_start: 0.9556 (tt) cc_final: 0.9239 (pp)
REVERT: B  171 LEU cc_start: 0.9802 (tt) cc_final: 0.9587 (tp)
REVERT: B  194 ASP cc_start: 0.9126 (p0) cc_final: 0.8440 (p0)
REVERT: B  225 TYR cc_start: 0.8827 (m-10) cc_final: 0.8509 (m-80)
REVERT: B  450 ASP cc_start: 0.9258 (t70) cc_final: 0.8985 (p0)
REVERT: B  457 MET cc_start: 0.9544 (mmp) cc_final: 0.9209 (ptt)
REVERT: C   86 PHE cc_start: 0.9151 (m-10) cc_final: 0.8848 (m-10)
REVERT: C   99 GLU cc_start: 0.8201 (pt0) cc_final: 0.7963 (pp20)
REVERT: C  109 ARG cc_start: 0.8236 (pmt-80) cc_final: 0.7966 (ptm-80)
REVERT: C  135 ILE cc_start: 0.9239 (tp) cc_final: 0.8974 (tp)
REVERT: C  140 ASP cc_start: 0.8051 (m-30) cc_final: 0.7002 (m-30)
REVERT: C  197 HIS cc_start: 0.9698 (t-170) cc_final: 0.9181 (t-170)
REVERT: D   28 PHE cc_start: 0.9139 (t80) cc_final: 0.8881 (t80)
REVERT: D   69 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8885 (tp)
  outliers start: 9
  outliers final: 2
  residues processed: 230
  average time/residue: 0.1958
  time to fit residues: 64.9321
Evaluate side-chains
  151 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 148
  time to evaluate  : 1.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 96 optimal weight:   10.0000
   chunk 117 optimal weight:   20.0000
   chunk 82 optimal weight:    6.9990
   chunk 110 optimal weight:   20.0000
   chunk 101 optimal weight:    3.9990
   chunk 18 optimal weight:    8.9990
   chunk 27 optimal weight:    9.9990
   chunk 21 optimal weight:    7.9990
   chunk 62 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   chunk 61 optimal weight:    3.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 420 GLN
** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 606 GLN
** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.049812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.042755 restraints weight = 78203.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.043701 restraints weight = 50407.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.044435 restraints weight = 37051.325|
|-----------------------------------------------------------------------------|
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.5036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   9894  Z= 0.347
  Angle     :  0.823  11.056  13488  Z= 0.429
  Chirality :  0.045   0.168   1560
  Planarity :  0.006   0.097   1680
  Dihedral  :  6.701  33.761   1319
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 20.60
  Ramachandran Plot:
    Outliers :  0.91 %
    Allowed  :  9.18 %
    Favored  : 89.91 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  6.52 %
    Favored  : 93.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 1.85 %
    Twisted General : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.12 (0.24), residues: 1209
  helix:  1.05 (0.19), residues: 688
  sheet: -2.59 (0.45), residues: 110
  loop : -3.45 (0.28), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A  84 
 HIS   0.009   0.002   HIS C  58 
 PHE   0.035   0.003   PHE A 302 
 TYR   0.023   0.002   TYR B 446 
 ARG   0.020   0.001   ARG A 659 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 182
  time to evaluate  : 1.035 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 MET cc_start: 0.8776 (mmt) cc_final: 0.8232 (mmt)
REVERT: A   97 LEU cc_start: 0.9441 (tp) cc_final: 0.9192 (tp)
REVERT: A  147 VAL cc_start: 0.8009 (OUTLIER) cc_final: 0.7581 (m)
REVERT: A  182 LEU cc_start: 0.9671 (tp) cc_final: 0.9217 (pp)
REVERT: A  347 MET cc_start: 0.9155 (mmp) cc_final: 0.8566 (tpp)
REVERT: A  378 MET cc_start: 0.8728 (mpp) cc_final: 0.8498 (mpp)
REVERT: A  457 TYR cc_start: 0.8324 (m-80) cc_final: 0.8096 (m-80)
REVERT: A  538 LEU cc_start: 0.9482 (mt) cc_final: 0.9119 (mt)
REVERT: A  657 ARG cc_start: 0.8918 (ptt-90) cc_final: 0.8099 (ptt90)
REVERT: A  675 VAL cc_start: 0.9223 (t) cc_final: 0.9004 (p)
REVERT: A  680 LEU cc_start: 0.9489 (tp) cc_final: 0.9275 (tt)
REVERT: B   92 CYS cc_start: 0.8843 (t) cc_final: 0.8004 (t)
REVERT: B  194 ASP cc_start: 0.9136 (p0) cc_final: 0.8470 (p0)
REVERT: B  225 TYR cc_start: 0.8898 (m-10) cc_final: 0.8561 (m-80)
REVERT: B  228 MET cc_start: 0.9524 (mpp) cc_final: 0.9314 (mmt)
REVERT: B  233 MET cc_start: 0.9055 (tpt) cc_final: 0.8784 (tpp)
REVERT: B  386 PHE cc_start: 0.8737 (t80) cc_final: 0.7725 (t80)
REVERT: B  391 VAL cc_start: 0.9539 (t) cc_final: 0.9279 (t)
REVERT: B  450 ASP cc_start: 0.9024 (t70) cc_final: 0.8819 (p0)
REVERT: B  457 MET cc_start: 0.9652 (mmp) cc_final: 0.9418 (mmm)
REVERT: C   86 PHE cc_start: 0.9219 (m-10) cc_final: 0.8904 (m-10)
REVERT: C  132 PHE cc_start: 0.9406 (m-10) cc_final: 0.9088 (m-10)
REVERT: C  140 ASP cc_start: 0.8733 (m-30) cc_final: 0.8255 (m-30)
REVERT: C  197 HIS cc_start: 0.9598 (t-170) cc_final: 0.9177 (t-170)
REVERT: C  205 PHE cc_start: 0.8914 (m-80) cc_final: 0.8688 (m-80)
REVERT: C  218 TYR cc_start: 0.9423 (m-80) cc_final: 0.9130 (m-80)
REVERT: D   69 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.8951 (tp)
  outliers start: 3
  outliers final: 1
  residues processed: 184
  average time/residue: 0.1982
  time to fit residues: 52.9380
Evaluate side-chains
  132 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 129
  time to evaluate  : 1.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 1 optimal weight:   20.0000
   chunk 82 optimal weight:    4.9990
   chunk 42 optimal weight:    9.9990
   chunk 106 optimal weight:    9.9990
   chunk 112 optimal weight:   20.0000
   chunk 83 optimal weight:    3.9990
   chunk 102 optimal weight:    6.9990
   chunk 48 optimal weight:    0.3980
   chunk 53 optimal weight:    0.9980
   chunk 55 optimal weight:    8.9990
   overall best weight:    2.4786

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

Flipped N/Q/H residues before XYZ refinement:
A 553 HIS
A 562 ASN
** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.050973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.043706 restraints weight = 74849.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.044713 restraints weight = 48384.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.045500 restraints weight = 35219.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.5607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9894  Z= 0.240
  Angle     :  0.756  11.287  13488  Z= 0.391
  Chirality :  0.044   0.209   1560
  Planarity :  0.006   0.091   1680
  Dihedral  :  6.173  32.823   1319
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 17.49
  Ramachandran Plot:
    Outliers :  0.91 %
    Allowed  :  7.03 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.84 %
    Favored  : 96.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 1.85 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (0.24), residues: 1209
  helix:  1.23 (0.19), residues: 695
  sheet: -2.28 (0.47), residues: 110
  loop : -3.27 (0.29), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP D  67 
 HIS   0.006   0.001   HIS A  74 
 PHE   0.032   0.002   PHE A 302 
 TYR   0.019   0.002   TYR C  90 
 ARG   0.004   0.000   ARG A 117 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 185
  time to evaluate  : 1.165 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 LEU cc_start: 0.9464 (tp) cc_final: 0.9226 (tp)
REVERT: A  182 LEU cc_start: 0.9663 (tp) cc_final: 0.9260 (pp)
REVERT: A  330 PHE cc_start: 0.8935 (m-80) cc_final: 0.8552 (m-80)
REVERT: A  347 MET cc_start: 0.9137 (mmp) cc_final: 0.8772 (mmp)
REVERT: A  378 MET cc_start: 0.8742 (mpp) cc_final: 0.8521 (mpp)
REVERT: A  538 LEU cc_start: 0.9419 (mt) cc_final: 0.9053 (mt)
REVERT: A  554 TYR cc_start: 0.8811 (t80) cc_final: 0.8572 (t80)
REVERT: A  677 PHE cc_start: 0.8940 (m-10) cc_final: 0.8672 (m-80)
REVERT: A  684 LEU cc_start: 0.9483 (mm) cc_final: 0.9254 (mm)
REVERT: B  194 ASP cc_start: 0.8867 (p0) cc_final: 0.8469 (p0)
REVERT: B  228 MET cc_start: 0.9471 (mpp) cc_final: 0.9157 (mmt)
REVERT: B  459 GLN cc_start: 0.9355 (tp40) cc_final: 0.9054 (tp40)
REVERT: C   84 GLU cc_start: 0.9354 (pp20) cc_final: 0.9026 (pp20)
REVERT: C   86 PHE cc_start: 0.9215 (m-10) cc_final: 0.8878 (m-10)
REVERT: C   99 GLU cc_start: 0.8645 (pt0) cc_final: 0.8387 (pp20)
REVERT: C  132 PHE cc_start: 0.9506 (m-10) cc_final: 0.8853 (m-10)
REVERT: C  199 LEU cc_start: 0.9276 (mm) cc_final: 0.9059 (pp)
REVERT: C  218 TYR cc_start: 0.9550 (m-80) cc_final: 0.9323 (m-80)
REVERT: D   28 PHE cc_start: 0.8869 (t80) cc_final: 0.8638 (t80)
REVERT: D   69 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.9010 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 186
  average time/residue: 0.1831
  time to fit residues: 50.9302
Evaluate side-chains
  130 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 129
  time to evaluate  : 1.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 17 optimal weight:    5.9990
   chunk 112 optimal weight:    6.9990
   chunk 87 optimal weight:    7.9990
   chunk 119 optimal weight:    6.9990
   chunk 80 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 105 optimal weight:   10.0000
   chunk 2 optimal weight:    0.6980
   chunk 84 optimal weight:    7.9990
   chunk 52 optimal weight:    0.5980
   chunk 90 optimal weight:   10.0000
   overall best weight:    2.4586

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

Flipped N/Q/H residues before XYZ refinement:
** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 454 GLN
C 197 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.050658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.043605 restraints weight = 74242.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.044552 restraints weight = 49912.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.045232 restraints weight = 37067.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.5931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9894  Z= 0.242
  Angle     :  0.733  11.279  13488  Z= 0.377
  Chirality :  0.043   0.187   1560
  Planarity :  0.006   0.088   1680
  Dihedral  :  5.907  30.934   1319
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 17.80
  Ramachandran Plot:
    Outliers :  0.83 %
    Allowed  :  8.44 %
    Favored  : 90.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 1.85 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.25), residues: 1209
  helix:  1.32 (0.19), residues: 695
  sheet: -2.24 (0.48), residues: 108
  loop : -3.12 (0.29), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP C  42 
 HIS   0.006   0.001   HIS C  58 
 PHE   0.036   0.002   PHE B 386 
 TYR   0.023   0.002   TYR A 457 
 ARG   0.005   0.000   ARG A 117 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 1.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 GLU cc_start: 0.9244 (pt0) cc_final: 0.8727 (tm-30)
REVERT: A  182 LEU cc_start: 0.9624 (tp) cc_final: 0.9245 (pp)
REVERT: A  213 CYS cc_start: 0.5295 (t) cc_final: 0.5061 (t)
REVERT: A  231 MET cc_start: 0.9481 (ttt) cc_final: 0.9236 (ttm)
REVERT: A  347 MET cc_start: 0.9145 (mmp) cc_final: 0.8725 (mmp)
REVERT: A  538 LEU cc_start: 0.9422 (mt) cc_final: 0.9042 (mt)
REVERT: A  554 TYR cc_start: 0.8790 (t80) cc_final: 0.8575 (t80)
REVERT: A  677 PHE cc_start: 0.8964 (m-10) cc_final: 0.8719 (m-80)
REVERT: A  684 LEU cc_start: 0.9450 (mm) cc_final: 0.9233 (mm)
REVERT: B  194 ASP cc_start: 0.9106 (p0) cc_final: 0.8339 (p0)
REVERT: B  195 TYR cc_start: 0.9194 (m-80) cc_final: 0.8928 (m-80)
REVERT: B  221 LEU cc_start: 0.8920 (mt) cc_final: 0.8219 (mt)
REVERT: B  225 TYR cc_start: 0.8938 (m-10) cc_final: 0.8614 (m-80)
REVERT: B  233 MET cc_start: 0.9233 (mmp) cc_final: 0.8810 (tpp)
REVERT: B  386 PHE cc_start: 0.8534 (t80) cc_final: 0.8171 (t80)
REVERT: B  457 MET cc_start: 0.9639 (mmp) cc_final: 0.9356 (mmp)
REVERT: B  459 GLN cc_start: 0.9201 (tp40) cc_final: 0.8918 (tp40)
REVERT: C   53 TRP cc_start: 0.8945 (t60) cc_final: 0.8677 (t60)
REVERT: C   84 GLU cc_start: 0.9356 (pp20) cc_final: 0.9037 (pp20)
REVERT: C   86 PHE cc_start: 0.9148 (m-10) cc_final: 0.8858 (m-10)
REVERT: C   99 GLU cc_start: 0.8630 (pt0) cc_final: 0.8389 (pp20)
REVERT: C  218 TYR cc_start: 0.9486 (m-80) cc_final: 0.9237 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 177
  average time/residue: 0.1823
  time to fit residues: 47.8025
Evaluate side-chains
  134 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 1.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 106 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 61 optimal weight:   10.0000
   chunk 54 optimal weight:   20.0000
   chunk 89 optimal weight:   10.0000
   chunk 73 optimal weight:    3.9990
   chunk 32 optimal weight:    6.9990
   chunk 107 optimal weight:    5.9990
   chunk 60 optimal weight:    0.0970
   chunk 36 optimal weight:    2.9990
   chunk 71 optimal weight:    7.9990
   overall best weight:    4.0186

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

Flipped N/Q/H residues before XYZ refinement:
A 449 HIS
** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.049181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.042371 restraints weight = 76150.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.043301 restraints weight = 49308.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.044022 restraints weight = 35701.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.6195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   9894  Z= 0.292
  Angle     :  0.771  11.525  13488  Z= 0.400
  Chirality :  0.044   0.227   1560
  Planarity :  0.006   0.083   1680
  Dihedral  :  5.934  29.878   1319
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 20.03
  Ramachandran Plot:
    Outliers :  0.83 %
    Allowed  :  8.77 %
    Favored  : 90.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.86 (0.24), residues: 1209
  helix:  1.11 (0.19), residues: 695
  sheet: -2.40 (0.46), residues: 115
  loop : -3.11 (0.29), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP B 244 
 HIS   0.007   0.002   HIS A 102 
 PHE   0.039   0.002   PHE C 205 
 TYR   0.022   0.002   TYR C  90 
 ARG   0.003   0.001   ARG A 117 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 1.084 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 GLU cc_start: 0.9247 (pt0) cc_final: 0.8703 (tm-30)
REVERT: A   95 MET cc_start: 0.8157 (mmp) cc_final: 0.7563 (mmp)
REVERT: A  103 PHE cc_start: 0.9249 (t80) cc_final: 0.8828 (t80)
REVERT: A  182 LEU cc_start: 0.9623 (tp) cc_final: 0.9176 (pp)
REVERT: A  213 CYS cc_start: 0.5124 (t) cc_final: 0.4699 (t)
REVERT: A  330 PHE cc_start: 0.9142 (m-80) cc_final: 0.8558 (m-80)
REVERT: A  347 MET cc_start: 0.9152 (mmp) cc_final: 0.8806 (mmp)
REVERT: A  538 LEU cc_start: 0.9385 (mt) cc_final: 0.8983 (tp)
REVERT: A  553 HIS cc_start: 0.8614 (m90) cc_final: 0.8375 (m90)
REVERT: A  554 TYR cc_start: 0.8801 (t80) cc_final: 0.8492 (t80)
REVERT: A  677 PHE cc_start: 0.8999 (m-10) cc_final: 0.8732 (m-80)
REVERT: A  681 ILE cc_start: 0.9682 (tp) cc_final: 0.9401 (tp)
REVERT: B  195 TYR cc_start: 0.9246 (m-80) cc_final: 0.9016 (m-80)
REVERT: B  225 TYR cc_start: 0.8882 (m-10) cc_final: 0.8643 (m-80)
REVERT: B  227 ILE cc_start: 0.9449 (pt) cc_final: 0.9210 (pt)
REVERT: B  228 MET cc_start: 0.9466 (mpp) cc_final: 0.9264 (mmt)
REVERT: B  386 PHE cc_start: 0.8609 (t80) cc_final: 0.8188 (t80)
REVERT: B  459 GLN cc_start: 0.9216 (tp40) cc_final: 0.8924 (tp40)
REVERT: C   53 TRP cc_start: 0.9012 (t60) cc_final: 0.8592 (t60)
REVERT: C   84 GLU cc_start: 0.9338 (pp20) cc_final: 0.9024 (pp20)
REVERT: C   86 PHE cc_start: 0.9209 (m-10) cc_final: 0.8921 (m-10)
REVERT: C   99 GLU cc_start: 0.8604 (pt0) cc_final: 0.8348 (pp20)
REVERT: C  119 TYR cc_start: 0.9189 (t80) cc_final: 0.8894 (t80)
REVERT: C  132 PHE cc_start: 0.9227 (m-10) cc_final: 0.8912 (m-10)
REVERT: C  218 TYR cc_start: 0.9504 (m-80) cc_final: 0.9188 (m-80)
REVERT: D   32 VAL cc_start: 0.9267 (t) cc_final: 0.9020 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.2019
  time to fit residues: 49.2726
Evaluate side-chains
  131 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 1.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 113 optimal weight:    0.9990
   chunk 80 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 55 optimal weight:    8.9990
   chunk 56 optimal weight:    0.1980
   chunk 93 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 65 optimal weight:   20.0000
   chunk 58 optimal weight:    8.9990
   chunk 89 optimal weight:    9.9990
   overall best weight:    2.8388

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

Flipped N/Q/H residues before XYZ refinement:
** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.049413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.042221 restraints weight = 74963.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.043205 restraints weight = 49472.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.043929 restraints weight = 36492.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.6415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9894  Z= 0.238
  Angle     :  0.737  11.490  13488  Z= 0.378
  Chirality :  0.043   0.181   1560
  Planarity :  0.006   0.080   1680
  Dihedral  :  5.740  29.274   1319
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 18.21
  Ramachandran Plot:
    Outliers :  0.83 %
    Allowed  :  7.94 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.68 (0.25), residues: 1209
  helix:  1.18 (0.19), residues: 696
  sheet: -1.93 (0.49), residues: 108
  loop : -3.05 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 244 
 HIS   0.006   0.001   HIS C  58 
 PHE   0.032   0.002   PHE C 205 
 TYR   0.018   0.002   TYR B 181 
 ARG   0.002   0.000   ARG A 434 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 1.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 GLU cc_start: 0.9307 (pt0) cc_final: 0.8658 (tm-30)
REVERT: A   95 MET cc_start: 0.7986 (mmp) cc_final: 0.7554 (mmt)
REVERT: A  182 LEU cc_start: 0.9570 (tp) cc_final: 0.9145 (pp)
REVERT: A  213 CYS cc_start: 0.5017 (t) cc_final: 0.4292 (t)
REVERT: A  347 MET cc_start: 0.9189 (mmp) cc_final: 0.8702 (mmp)
REVERT: A  430 PHE cc_start: 0.8898 (m-80) cc_final: 0.8586 (m-80)
REVERT: A  538 LEU cc_start: 0.9427 (mt) cc_final: 0.9062 (mt)
REVERT: A  554 TYR cc_start: 0.8818 (t80) cc_final: 0.8531 (t80)
REVERT: A  677 PHE cc_start: 0.9043 (m-10) cc_final: 0.8712 (m-80)
REVERT: B  195 TYR cc_start: 0.9270 (m-80) cc_final: 0.8987 (m-80)
REVERT: B  221 LEU cc_start: 0.8798 (mt) cc_final: 0.8120 (mt)
REVERT: B  227 ILE cc_start: 0.9446 (pt) cc_final: 0.9189 (pt)
REVERT: B  228 MET cc_start: 0.9527 (mpp) cc_final: 0.9262 (mmt)
REVERT: B  386 PHE cc_start: 0.8474 (t80) cc_final: 0.8242 (t80)
REVERT: B  457 MET cc_start: 0.9575 (mmp) cc_final: 0.9255 (mmm)
REVERT: B  459 GLN cc_start: 0.9241 (tp40) cc_final: 0.8971 (tp40)
REVERT: C    9 CYS cc_start: 0.9637 (m) cc_final: 0.8998 (p)
REVERT: C   53 TRP cc_start: 0.8950 (t60) cc_final: 0.8570 (t60)
REVERT: C   84 GLU cc_start: 0.9332 (pp20) cc_final: 0.9045 (pp20)
REVERT: C   86 PHE cc_start: 0.9235 (m-10) cc_final: 0.8963 (m-10)
REVERT: C   98 ASP cc_start: 0.9477 (t0) cc_final: 0.9148 (m-30)
REVERT: C   99 GLU cc_start: 0.8604 (pt0) cc_final: 0.8278 (pp20)
REVERT: C  119 TYR cc_start: 0.9183 (t80) cc_final: 0.8916 (t80)
REVERT: C  132 PHE cc_start: 0.9281 (m-10) cc_final: 0.9062 (m-10)
REVERT: C  167 ILE cc_start: 0.9758 (tt) cc_final: 0.9469 (tt)
REVERT: C  171 HIS cc_start: 0.9517 (m90) cc_final: 0.8800 (m90)
REVERT: C  218 TYR cc_start: 0.9500 (m-80) cc_final: 0.9102 (m-80)
REVERT: D   28 PHE cc_start: 0.8906 (t80) cc_final: 0.8705 (t80)
REVERT: D   32 VAL cc_start: 0.9255 (t) cc_final: 0.9033 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 167
  average time/residue: 0.1912
  time to fit residues: 47.1589
Evaluate side-chains
  130 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 1.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 85 optimal weight:    0.7980
   chunk 52 optimal weight:    0.0770
   chunk 46 optimal weight:    8.9990
   chunk 114 optimal weight:    9.9990
   chunk 16 optimal weight:    4.9990
   chunk 110 optimal weight:    4.9990
   chunk 70 optimal weight:    7.9990
   chunk 116 optimal weight:   20.0000
   chunk 66 optimal weight:    8.9990
   chunk 5 optimal weight:    5.9990
   chunk 18 optimal weight:    7.9990
   overall best weight:    3.3744

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

Flipped N/Q/H residues before XYZ refinement:
** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 454 GLN
** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.048876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.041878 restraints weight = 76706.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.042865 restraints weight = 50141.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.043563 restraints weight = 36785.548|
|-----------------------------------------------------------------------------|
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.6581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9894  Z= 0.263
  Angle     :  0.757  11.654  13488  Z= 0.392
  Chirality :  0.044   0.172   1560
  Planarity :  0.006   0.079   1680
  Dihedral  :  5.765  28.799   1319
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 19.10
  Ramachandran Plot:
    Outliers :  0.83 %
    Allowed  :  8.11 %
    Favored  : 91.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (0.24), residues: 1209
  helix:  1.03 (0.19), residues: 694
  sheet: -1.83 (0.50), residues: 108
  loop : -2.99 (0.29), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP D  67 
 HIS   0.006   0.002   HIS C  58 
 PHE   0.033   0.002   PHE A 181 
 TYR   0.025   0.002   TYR A 565 
 ARG   0.003   0.000   ARG C 184 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 1.292 
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: symmetry clash
REVERT: A   95 MET cc_start: 0.8127 (mmp) cc_final: 0.7720 (mmt)
REVERT: A   97 LEU cc_start: 0.9363 (tp) cc_final: 0.9110 (tp)
REVERT: A  182 LEU cc_start: 0.9518 (tp) cc_final: 0.9074 (pp)
REVERT: A  347 MET cc_start: 0.9168 (mmp) cc_final: 0.8667 (mmp)
REVERT: A  378 MET cc_start: 0.8707 (mpp) cc_final: 0.8504 (mpp)
REVERT: A  430 PHE cc_start: 0.8894 (m-80) cc_final: 0.8559 (m-80)
REVERT: A  538 LEU cc_start: 0.9437 (mt) cc_final: 0.9033 (tp)
REVERT: A  554 TYR cc_start: 0.8807 (t80) cc_final: 0.8538 (t80)
REVERT: B  195 TYR cc_start: 0.9262 (m-80) cc_final: 0.8963 (m-80)
REVERT: B  225 TYR cc_start: 0.8985 (m-80) cc_final: 0.8668 (m-80)
REVERT: B  386 PHE cc_start: 0.8493 (t80) cc_final: 0.8170 (t80)
REVERT: B  457 MET cc_start: 0.9550 (mmp) cc_final: 0.9262 (mmm)
REVERT: B  459 GLN cc_start: 0.9239 (tp40) cc_final: 0.8940 (tp40)
REVERT: C    9 CYS cc_start: 0.9662 (m) cc_final: 0.9041 (p)
REVERT: C   53 TRP cc_start: 0.8985 (t60) cc_final: 0.8549 (t60)
REVERT: C   84 GLU cc_start: 0.9340 (pp20) cc_final: 0.9060 (pp20)
REVERT: C   86 PHE cc_start: 0.9224 (m-10) cc_final: 0.8943 (m-10)
REVERT: C   99 GLU cc_start: 0.8569 (pt0) cc_final: 0.8303 (pp20)
REVERT: C  109 ARG cc_start: 0.8289 (pmt-80) cc_final: 0.7712 (ptm-80)
REVERT: C  119 TYR cc_start: 0.9205 (t80) cc_final: 0.8923 (t80)
REVERT: C  132 PHE cc_start: 0.9317 (m-10) cc_final: 0.9048 (m-10)
REVERT: C  167 ILE cc_start: 0.9753 (tt) cc_final: 0.9396 (tt)
REVERT: C  171 HIS cc_start: 0.9478 (m90) cc_final: 0.8697 (m90)
REVERT: C  218 TYR cc_start: 0.9525 (m-80) cc_final: 0.9070 (m-80)
REVERT: D   28 PHE cc_start: 0.8966 (t80) cc_final: 0.8707 (t80)
REVERT: D   32 VAL cc_start: 0.9274 (t) cc_final: 0.9040 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.2045
  time to fit residues: 49.9293
Evaluate side-chains
  128 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 1.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 72 optimal weight:    9.9990
   chunk 114 optimal weight:    1.9990
   chunk 73 optimal weight:   10.0000
   chunk 21 optimal weight:    6.9990
   chunk 28 optimal weight:    4.9990
   chunk 56 optimal weight:    0.0870
   chunk 112 optimal weight:   10.0000
   chunk 85 optimal weight:    6.9990
   chunk 108 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    2.4166

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

Flipped N/Q/H residues before XYZ refinement:
** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.049510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.042522 restraints weight = 74490.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.043487 restraints weight = 49606.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.044067 restraints weight = 36621.345|
|-----------------------------------------------------------------------------|
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.6741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9894  Z= 0.230
  Angle     :  0.751  11.665  13488  Z= 0.384
  Chirality :  0.044   0.244   1560
  Planarity :  0.006   0.080   1680
  Dihedral  :  5.601  29.028   1319
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 16.40
  Ramachandran Plot:
    Outliers :  0.83 %
    Allowed  :  7.44 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.25), residues: 1209
  helix:  1.02 (0.19), residues: 695
  sheet: -1.74 (0.50), residues: 108
  loop : -2.92 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP B 404 
 HIS   0.006   0.001   HIS C 197 
 PHE   0.031   0.002   PHE A 181 
 TYR   0.020   0.002   TYR A 565 
 ARG   0.002   0.000   ARG D  82 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 1.093 
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   97 LEU cc_start: 0.9391 (tp) cc_final: 0.9152 (tp)
REVERT: A  182 LEU cc_start: 0.9494 (tp) cc_final: 0.9034 (pp)
REVERT: A  213 CYS cc_start: 0.4401 (t) cc_final: 0.3736 (t)
REVERT: A  347 MET cc_start: 0.9200 (mmp) cc_final: 0.8685 (mmp)
REVERT: A  378 MET cc_start: 0.8717 (mpp) cc_final: 0.8494 (mpp)
REVERT: A  430 PHE cc_start: 0.8888 (m-80) cc_final: 0.8564 (m-80)
REVERT: A  538 LEU cc_start: 0.9418 (mt) cc_final: 0.9017 (tp)
REVERT: A  553 HIS cc_start: 0.8636 (m90) cc_final: 0.8315 (m90)
REVERT: A  554 TYR cc_start: 0.8769 (t80) cc_final: 0.8549 (t80)
REVERT: A  677 PHE cc_start: 0.9300 (m-10) cc_final: 0.8992 (m-80)
REVERT: B   84 MET cc_start: 0.9288 (mpp) cc_final: 0.9059 (mpp)
REVERT: B  195 TYR cc_start: 0.9268 (m-80) cc_final: 0.8976 (m-80)
REVERT: B  386 PHE cc_start: 0.8556 (t80) cc_final: 0.8280 (t80)
REVERT: B  459 GLN cc_start: 0.9246 (tp40) cc_final: 0.8941 (tp40)
REVERT: C    9 CYS cc_start: 0.9673 (m) cc_final: 0.9067 (p)
REVERT: C   11 PHE cc_start: 0.9260 (m-10) cc_final: 0.9052 (m-80)
REVERT: C   53 TRP cc_start: 0.9003 (t60) cc_final: 0.8598 (t60)
REVERT: C   84 GLU cc_start: 0.9313 (pp20) cc_final: 0.9055 (pp20)
REVERT: C   86 PHE cc_start: 0.9255 (m-10) cc_final: 0.9014 (m-10)
REVERT: C   99 GLU cc_start: 0.8572 (pt0) cc_final: 0.8305 (pp20)
REVERT: C  119 TYR cc_start: 0.9189 (t80) cc_final: 0.8903 (t80)
REVERT: C  132 PHE cc_start: 0.9243 (m-10) cc_final: 0.9021 (m-10)
REVERT: C  140 ASP cc_start: 0.8633 (m-30) cc_final: 0.8414 (m-30)
REVERT: C  167 ILE cc_start: 0.9742 (tt) cc_final: 0.9440 (tt)
REVERT: C  171 HIS cc_start: 0.9467 (m90) cc_final: 0.8746 (m90)
REVERT: C  218 TYR cc_start: 0.9519 (m-80) cc_final: 0.8977 (m-80)
REVERT: D   28 PHE cc_start: 0.8931 (t80) cc_final: 0.8670 (t80)
REVERT: D   32 VAL cc_start: 0.9290 (t) cc_final: 0.9066 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.1890
  time to fit residues: 46.0053
Evaluate side-chains
  131 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 1.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 95 optimal weight:    9.9990
   chunk 21 optimal weight:    7.9990
   chunk 61 optimal weight:    4.9990
   chunk 39 optimal weight:   10.0000
   chunk 5 optimal weight:    9.9990
   chunk 38 optimal weight:    4.9990
   chunk 101 optimal weight:    0.8980
   chunk 109 optimal weight:    9.9990
   chunk 59 optimal weight:    9.9990
   chunk 112 optimal weight:   20.0000
   chunk 37 optimal weight:    0.2980
   overall best weight:    3.8386

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

Flipped N/Q/H residues before XYZ refinement:
A 379 HIS
** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.048340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.041357 restraints weight = 76286.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.042321 restraints weight = 50215.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.043006 restraints weight = 36880.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.6833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9894  Z= 0.286
  Angle     :  0.774  11.705  13488  Z= 0.399
  Chirality :  0.044   0.213   1560
  Planarity :  0.006   0.081   1680
  Dihedral  :  5.748  28.590   1319
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 18.84
  Ramachandran Plot:
    Outliers :  0.83 %
    Allowed  :  8.19 %
    Favored  : 90.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.24), residues: 1209
  helix:  0.99 (0.19), residues: 695
  sheet: -1.77 (0.48), residues: 108
  loop : -2.90 (0.29), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 404 
 HIS   0.007   0.002   HIS C  58 
 PHE   0.030   0.002   PHE A 302 
 TYR   0.023   0.002   TYR C  90 
 ARG   0.004   0.000   ARG C 109 

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 1.012 
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  182 LEU cc_start: 0.9462 (tp) cc_final: 0.8960 (pp)
REVERT: A  347 MET cc_start: 0.9214 (mmp) cc_final: 0.8733 (mmp)
REVERT: A  378 MET cc_start: 0.8746 (mpp) cc_final: 0.8545 (mpp)
REVERT: A  430 PHE cc_start: 0.8953 (m-80) cc_final: 0.8616 (m-80)
REVERT: A  538 LEU cc_start: 0.9379 (mt) cc_final: 0.8968 (tp)
REVERT: A  553 HIS cc_start: 0.8605 (m90) cc_final: 0.8311 (m90)
REVERT: A  554 TYR cc_start: 0.8700 (t80) cc_final: 0.8439 (t80)
REVERT: A  677 PHE cc_start: 0.9305 (m-10) cc_final: 0.8996 (m-80)
REVERT: B  195 TYR cc_start: 0.9269 (m-80) cc_final: 0.9030 (m-80)
REVERT: B  386 PHE cc_start: 0.8452 (t80) cc_final: 0.8026 (t80)
REVERT: B  457 MET cc_start: 0.9616 (mmp) cc_final: 0.9399 (mmp)
REVERT: B  459 GLN cc_start: 0.9265 (tp40) cc_final: 0.8970 (tp40)
REVERT: C    9 CYS cc_start: 0.9690 (m) cc_final: 0.9067 (p)
REVERT: C   11 PHE cc_start: 0.9222 (m-10) cc_final: 0.8985 (m-80)
REVERT: C   53 TRP cc_start: 0.9020 (t60) cc_final: 0.8538 (t60)
REVERT: C   84 GLU cc_start: 0.9305 (pp20) cc_final: 0.9051 (pp20)
REVERT: C   86 PHE cc_start: 0.9232 (m-10) cc_final: 0.8991 (m-10)
REVERT: C   98 ASP cc_start: 0.9491 (t0) cc_final: 0.9142 (m-30)
REVERT: C   99 GLU cc_start: 0.8504 (pt0) cc_final: 0.8075 (pp20)
REVERT: C  119 TYR cc_start: 0.9205 (t80) cc_final: 0.8947 (t80)
REVERT: C  132 PHE cc_start: 0.9250 (m-10) cc_final: 0.9045 (m-10)
REVERT: C  140 ASP cc_start: 0.8566 (m-30) cc_final: 0.8345 (m-30)
REVERT: C  167 ILE cc_start: 0.9749 (tt) cc_final: 0.9384 (tt)
REVERT: C  171 HIS cc_start: 0.9460 (m90) cc_final: 0.8677 (m90)
REVERT: C  218 TYR cc_start: 0.9536 (m-80) cc_final: 0.8957 (m-80)
REVERT: D   28 PHE cc_start: 0.8875 (t80) cc_final: 0.8478 (t80)
REVERT: D   32 VAL cc_start: 0.9314 (t) cc_final: 0.8990 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 163
  average time/residue: 0.1862
  time to fit residues: 45.3268
Evaluate side-chains
  131 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 1.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 71 optimal weight:   10.0000
   chunk 31 optimal weight:    9.9990
   chunk 13 optimal weight:    7.9990
   chunk 103 optimal weight:    2.9990
   chunk 54 optimal weight:    4.9990
   chunk 120 optimal weight:   20.0000
   chunk 50 optimal weight:    7.9990
   chunk 37 optimal weight:    0.2980
   chunk 109 optimal weight:    9.9990
   chunk 118 optimal weight:    7.9990
   chunk 105 optimal weight:    8.9990
   overall best weight:    4.8588

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

Flipped N/Q/H residues before XYZ refinement:
** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.047516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.040513 restraints weight = 76763.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.041493 restraints weight = 49767.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.042172 restraints weight = 36511.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.6885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   9894  Z= 0.326
  Angle     :  0.801  11.744  13488  Z= 0.416
  Chirality :  0.045   0.228   1560
  Planarity :  0.006   0.089   1680
  Dihedral  :  5.879  29.003   1319
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 21.33
  Ramachandran Plot:
    Outliers :  0.83 %
    Allowed  :  8.68 %
    Favored  : 90.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.26 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.97 (0.24), residues: 1209
  helix:  0.83 (0.19), residues: 690
  sheet: -2.07 (0.46), residues: 113
  loop : -2.86 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 404 
 HIS   0.007   0.002   HIS C  58 
 PHE   0.030   0.002   PHE A 302 
 TYR   0.024   0.002   TYR C  90 
 ARG   0.004   0.001   ARG A 434 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2608.67 seconds
wall clock time: 47 minutes 55.82 seconds (2875.82 seconds total)