Starting phenix.real_space_refine
on Tue Jun 10 14:09:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qe5_13930/06_2025/7qe5_13930_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qe5_13930/06_2025/7qe5_13930.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qe5_13930/06_2025/7qe5_13930.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qe5_13930/06_2025/7qe5_13930.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qe5_13930/06_2025/7qe5_13930_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qe5_13930/06_2025/7qe5_13930_neut.cif"
  }
  resolution = 4.7
  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=   0.001 sd=   0.024
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: 5
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    3793      2.51       5
     N     905      2.21       5
     O     985      1.98       5
     H    5932      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 11652
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 616, 9794
          Classifications: {'peptide': 616}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 588}
    Chain: "B"
      Number of atoms: 1858
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 1858
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 3, 'TRANS': 120}
          Chain breaks: 1
  Time building chain proxies: 6.83, per 1000 atoms: 0.59
  Number of scatterers: 11652
  At special positions: 0
  Unit cell: (108.36, 94.6, 86, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      37     16.00
     O     985      8.00
     N     905      7.00
     C    3793      6.00
     H    5932      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 460 " - pdb=" SG  CYS B 534 " distance=2.06

  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: 4.13
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1360

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 2 sheets defined
      74.9% alpha, 3.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 5
    Processing helix  chain 'A' and resid 6 through 33
      removed outlier: 3.527A  pdb=" N   LEU A  28 " --> pdb=" O   ILE A  24 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   GLN A  31 " --> pdb=" O   ILE A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 62
      removed outlier: 3.661A  pdb=" N   GLU A  42 " --> pdb=" O   ILE A  38 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   LYS A  45 " --> pdb=" O   GLU A  41 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LEU A  46 " --> pdb=" O   GLU A  42 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   VAL A  49 " --> pdb=" O   LYS A  45 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   TYR A  50 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 75
      removed outlier: 3.873A  pdb=" N   ASN A  73 " --> pdb=" O   ASP A  69 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LEU A  74 " --> pdb=" O   PHE A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 107
      removed outlier: 3.884A  pdb=" N   PHE A  96 " --> pdb=" O   PHE A  92 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ASN A 107 " --> pdb=" O   ILE A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 117
    Processing helix  chain 'A' and resid 121 through 149
      removed outlier: 4.355A  pdb=" N   PHE A 125 " --> pdb=" O   GLU A 121 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   LEU A 128 " --> pdb=" O   ILE A 124 " (cutoff:3.500A)
      Proline residue:  A 129  - end of helix
    Processing helix  chain 'A' and resid 155 through 173
      removed outlier: 4.073A  pdb=" N   PHE A 159 " --> pdb=" O   PRO A 155 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LEU A 170 " --> pdb=" O   LEU A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 179
    Processing helix  chain 'A' and resid 180 through 186
      removed outlier: 6.301A  pdb=" N   SER A 183 " --> pdb=" O   LEU A 180 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   ASN A 184 " --> pdb=" O   ARG A 181 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   ILE A 186 " --> pdb=" O   SER A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 190
      No H-bonds generated for 'chain 'A' and resid 188 through 190'
    Processing helix  chain 'A' and resid 191 through 206
    Processing helix  chain 'A' and resid 209 through 225
      removed outlier: 3.720A  pdb=" N   PHE A 222 " --> pdb=" O   THR A 218 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   SER A 223 " --> pdb=" O   LEU A 219 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   MET A 224 " --> pdb=" O   LEU A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 241
      removed outlier: 3.879A  pdb=" N   THR A 234 " --> pdb=" O   VAL A 230 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   LYS A 236 " --> pdb=" O   ALA A 232 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   VAL A 238 " --> pdb=" O   THR A 234 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   TYR A 239 " --> pdb=" O   GLU A 235 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   LEU A 241 " --> pdb=" O   LEU A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 262
      removed outlier: 4.109A  pdb=" N   ALA A 248 " --> pdb=" O   PHE A 244 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   VAL A 249 " --> pdb=" O   PRO A 245 " (cutoff:3.500A)
      Proline residue:  A 250  - end of helix
    Processing helix  chain 'A' and resid 263 through 276
      removed outlier: 4.280A  pdb=" N   ARG A 267 " --> pdb=" O   GLY A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 299
      removed outlier: 4.137A  pdb=" N   LEU A 292 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   LEU A 293 " --> pdb=" O   GLY A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 320
      removed outlier: 5.585A  pdb=" N   GLN A 310 " --> pdb=" O   GLY A 306 " (cutoff:3.500A)
      removed outlier: 5.342A  pdb=" N   LEU A 311 " --> pdb=" O   GLY A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 340
      removed outlier: 3.504A  pdb=" N   GLY A 337 " --> pdb=" O   SER A 333 " (cutoff:3.500A)
      Proline residue:  A 338  - end of helix
    Processing helix  chain 'A' and resid 343 through 354
    Processing helix  chain 'A' and resid 356 through 387
      removed outlier: 3.501A  pdb=" N   LEU A 360 " --> pdb=" O   SER A 356 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ALA A 363 " --> pdb=" O   LYS A 359 " (cutoff:3.500A)
      removed outlier: 4.986A  pdb=" N   ILE A 366 " --> pdb=" O   ILE A 362 " (cutoff:3.500A)
      Proline residue:  A 367  - end of helix
      removed outlier: 4.247A  pdb=" N   LYS A 385 " --> pdb=" O   ARG A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 395 through 422
      removed outlier: 4.229A  pdb=" N   TRP A 408 " --> pdb=" O   LYS A 404 " (cutoff:3.500A)
      removed outlier: 5.617A  pdb=" N   ALA A 409 " --> pdb=" O   GLN A 405 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   LEU A 411 " --> pdb=" O   PHE A 407 " (cutoff:3.500A)
      removed outlier: 5.374A  pdb=" N   THR A 412 " --> pdb=" O   TRP A 408 " (cutoff:3.500A)
      Proline residue:  A 413  - end of helix
      removed outlier: 3.574A  pdb=" N   ILE A 416 " --> pdb=" O   THR A 412 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ILE A 420 " --> pdb=" O   ILE A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 445
    Processing helix  chain 'A' and resid 452 through 486
      removed outlier: 3.537A  pdb=" N   GLU A 460 " --> pdb=" O   ASN A 456 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   VAL A 467 " --> pdb=" O   ALA A 463 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   ASP A 480 " --> pdb=" O   THR A 476 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   MET A 481 " --> pdb=" O   PHE A 477 " (cutoff:3.500A)
      removed outlier: 5.007A  pdb=" N   ALA A 483 " --> pdb=" O   GLY A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 486 through 497
      removed outlier: 3.738A  pdb=" N   ARG A 490 " --> pdb=" O   GLN A 486 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   VAL A 494 " --> pdb=" O   ARG A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 518
      removed outlier: 3.504A  pdb=" N   VAL A 505 " --> pdb=" O   SER A 501 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 521 through 540
      removed outlier: 5.206A  pdb=" N   PHE A 527 " --> pdb=" O   LEU A 523 " (cutoff:3.500A)
      Proline residue:  A 531  - end of helix
      Proline residue:  A 535  - end of helix
    Processing helix  chain 'A' and resid 543 through 560
      removed outlier: 3.504A  pdb=" N   VAL A 549 " --> pdb=" O   ILE A 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 576
      removed outlier: 3.783A  pdb=" N   PHE A 569 " --> pdb=" O   GLY A 565 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 587
      removed outlier: 3.652A  pdb=" N   LYS A 584 " --> pdb=" O   SER A 580 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 589 through 603
      removed outlier: 3.578A  pdb=" N   VAL A 593 " --> pdb=" O   PHE A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 615
      removed outlier: 4.141A  pdb=" N   VAL A 610 " --> pdb=" O   ILE A 606 " (cutoff:3.500A)
      Proline residue:  A 611  - end of helix
    Processing helix  chain 'B' and resid 525 through 529
    Processing sheet with id=AA1, first strand: chain 'B' and resid 38 through 40
      removed outlier: 3.708A  pdb=" N   LEU B 456 " --> pdb=" O   MET B 521 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 473 through 477
      removed outlier: 4.384A  pdb=" N   ALA B 530 " --> pdb=" O   VAL B 559 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   VAL B 559 " --> pdb=" O   ALA B 530 " (cutoff:3.500A)

    366 hydrogen bonds defined for protein.
    1068 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: 4.64

  Time building geometry restraints manager: 4.94 seconds

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

  Histogram of bond lengths:
        0.95 -     1.13: 5927
        1.13 -     1.30: 903
        1.30 -     1.48: 2290
        1.48 -     1.65: 2601
        1.65 -     1.83: 67
  Bond restraints: 11788
  Sorted by residual:
  bond pdb=" N   ARG B 483 "
       pdb=" H   ARG B 483 "
    ideal  model  delta    sigma   weight residual
    0.860  1.036 -0.176 2.00e-02 2.50e+03 7.78e+01
  bond pdb=" N   SER B 543 "
       pdb=" H   SER B 543 "
    ideal  model  delta    sigma   weight residual
    0.860  1.036 -0.176 2.00e-02 2.50e+03 7.76e+01
  bond pdb=" N   ARG A  80 "
       pdb=" H   ARG A  80 "
    ideal  model  delta    sigma   weight residual
    0.860  1.036 -0.176 2.00e-02 2.50e+03 7.76e+01
  bond pdb=" N   TYR B 552 "
       pdb=" H   TYR B 552 "
    ideal  model  delta    sigma   weight residual
    0.860  1.036 -0.176 2.00e-02 2.50e+03 7.75e+01
  bond pdb=" N   TRP B 553 "
       pdb=" H   TRP B 553 "
    ideal  model  delta    sigma   weight residual
    0.860  1.036 -0.176 2.00e-02 2.50e+03 7.75e+01
  ... (remaining 11783 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.65: 20286
        4.65 -     9.31: 1049
        9.31 -    13.96: 36
       13.96 -    18.62: 4
       18.62 -    23.27: 1
  Bond angle restraints: 21376
  Sorted by residual:
  angle pdb=" C   TYR B 550 "
        pdb=" CA  TYR B 550 "
        pdb=" CB  TYR B 550 "
      ideal   model   delta    sigma   weight residual
     110.68   87.41   23.27 1.70e+00 3.46e-01 1.87e+02
  angle pdb=" CA  ASP B 471 "
        pdb=" CB  ASP B 471 "
        pdb=" CG  ASP B 471 "
      ideal   model   delta    sigma   weight residual
     112.60  122.37   -9.77 1.00e+00 1.00e+00 9.55e+01
  angle pdb=" C   PRO A  76 "
        pdb=" CA  PRO A  76 "
        pdb=" CB  PRO A  76 "
      ideal   model   delta    sigma   weight residual
     111.22   97.57   13.65 1.51e+00 4.39e-01 8.17e+01
  angle pdb=" CA  PHE A 222 "
        pdb=" CB  PHE A 222 "
        pdb=" CG  PHE A 222 "
      ideal   model   delta    sigma   weight residual
     113.80  122.71   -8.91 1.00e+00 1.00e+00 7.94e+01
  angle pdb=" N   TYR B 552 "
        pdb=" CA  TYR B 552 "
        pdb=" C   TYR B 552 "
      ideal   model   delta    sigma   weight residual
     108.14  121.26  -13.12 1.52e+00 4.33e-01 7.45e+01
  ... (remaining 21371 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.40: 4908
       17.40 -    34.79: 394
       34.79 -    52.19: 113
       52.19 -    69.58: 116
       69.58 -    86.98: 11
  Dihedral angle restraints: 5542
    sinusoidal: 2956
      harmonic: 2586
  Sorted by residual:
  dihedral pdb=" C   TYR B 550 "
           pdb=" N   TYR B 550 "
           pdb=" CA  TYR B 550 "
           pdb=" CB  TYR B 550 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -103.61  -18.99     0      2.50e+00 1.60e-01 5.77e+01
  dihedral pdb=" C   ILE A 615 "
           pdb=" N   ILE A 615 "
           pdb=" CA  ILE A 615 "
           pdb=" CB  ILE A 615 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -139.87   17.87     0      2.50e+00 1.60e-01 5.11e+01
  dihedral pdb=" CD  ARG B 536 "
           pdb=" NE  ARG B 536 "
           pdb=" CZ  ARG B 536 "
           pdb=" NH1 ARG B 536 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   57.93  -57.93     1      1.00e+01 1.00e-02 4.50e+01
  ... (remaining 5539 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.112: 706
       0.112 -    0.224: 195
       0.224 -    0.336: 33
       0.336 -    0.448: 7
       0.448 -    0.560: 2
  Chirality restraints: 943
  Sorted by residual:
  chirality pdb=" CA  ILE A 615 "
            pdb=" N   ILE A 615 "
            pdb=" C   ILE A 615 "
            pdb=" CB  ILE A 615 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    1.87    0.56 2.00e-01 2.50e+01 7.85e+00
  chirality pdb=" CA  GLN A 143 "
            pdb=" N   GLN A 143 "
            pdb=" C   GLN A 143 "
            pdb=" CB  GLN A 143 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.77e+00
  chirality pdb=" CA  HIS B 470 "
            pdb=" N   HIS B 470 "
            pdb=" C   HIS B 470 "
            pdb=" CB  HIS B 470 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.66e+00
  ... (remaining 940 not shown)

  Planarity restraints: 1680
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 536 "    1.338 9.50e-02 1.11e+02   4.59e-01 4.67e+02
        pdb=" NE  ARG B 536 "    0.132 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 536 "   -0.020 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 536 "   -0.038 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 536 "   -0.068 2.00e-02 2.50e+03
        pdb="HH11 ARG B 536 "   -0.187 2.00e-02 2.50e+03
        pdb="HH12 ARG B 536 "    0.149 2.00e-02 2.50e+03
        pdb="HH21 ARG B 536 "   -0.128 2.00e-02 2.50e+03
        pdb="HH22 ARG B 536 "    0.100 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 546 "   -0.124 2.00e-02 2.50e+03   1.36e-01 2.78e+02
        pdb=" CG  ASN B 546 "    0.003 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 546 "    0.143 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 546 "   -0.076 2.00e-02 2.50e+03
        pdb="HD21 ASN B 546 "    0.211 2.00e-02 2.50e+03
        pdb="HD22 ASN B 546 "   -0.157 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN B 477 "   -0.128 2.00e-02 2.50e+03   1.23e-01 2.27e+02
        pdb=" CD  GLN B 477 "    0.020 2.00e-02 2.50e+03
        pdb=" OE1 GLN B 477 "    0.103 2.00e-02 2.50e+03
        pdb=" NE2 GLN B 477 "    0.083 2.00e-02 2.50e+03
        pdb="HE21 GLN B 477 "    0.125 2.00e-02 2.50e+03
        pdb="HE22 GLN B 477 "   -0.203 2.00e-02 2.50e+03
  ... (remaining 1677 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.19: 725
        2.19 -     2.79: 21236
        2.79 -     3.39: 33116
        3.39 -     4.00: 41706
        4.00 -     4.60: 60408
  Nonbonded interactions: 157191
  Sorted by model distance:
  nonbonded pdb=" O   THR A 330 "
            pdb=" HG  SER A 333 "
     model   vdw
     1.586 2.450
  nonbonded pdb=" HG  SER A 426 "
            pdb=" OE2 GLU A 429 "
     model   vdw
     1.609 2.450
  nonbonded pdb=" HH  TYR A 221 "
            pdb=" OE2 GLU A 485 "
     model   vdw
     1.616 2.450
  nonbonded pdb=" O   LEU A  54 "
            pdb=" HG  SER A  57 "
     model   vdw
     1.622 2.450
  nonbonded pdb=" OD1 ASP B 468 "
            pdb=" HG  SER B 491 "
     model   vdw
     1.632 2.450
  ... (remaining 157186 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=0.00 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:             0.870
  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:             0.190
  Extract box with map and model:          0.610
  Check model and map are aligned:         0.120
  Set scattering table:                    0.170
  Process input model:                     34.100
  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:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6985
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      :  0.013   0.092   5857  Z= 0.801
  Angle     :  2.056  23.272   7957  Z= 1.372
  Chirality :  0.108   0.560    943
  Planarity :  0.023   0.473    973
  Dihedral  : 14.367  86.978   2058
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.77 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  8.28 %
    Favored  : 90.58 %
  Cbeta Deviations :  2.50 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    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: -2.59 (0.26), residues: 734
  helix: -1.69 (0.18), residues: 471
  sheet: -1.82 (1.41), residues: 15
  loop : -1.37 (0.39), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.099   0.023   TRP A 227 
 HIS   0.010   0.004   HIS A  65 
 PHE   0.107   0.015   PHE A  48 
 TYR   0.152   0.026   TYR A 252 
 ARG   0.022   0.002   ARG B 536 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18515 (  366)
  hydrogen bonds       : angle       8.15751 ( 1068)
  SS BOND              : bond        0.02687 (    1)
  SS BOND              : angle       1.06634 (    2)
  covalent geometry    : bond        0.01316 ( 5856)
  covalent geometry    : angle       2.05573 ( 7955)

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 214
  time to evaluate  : 0.938 
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: 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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.8233 (tpt) cc_final: 0.8028 (tpp)
REVERT: A   27 ILE cc_start: 0.9196 (tp) cc_final: 0.8806 (tp)
REVERT: A   63 GLN cc_start: 0.8598 (tp40) cc_final: 0.7780 (mt0)
REVERT: A   78 LYS cc_start: 0.2644 (OUTLIER) cc_final: 0.2330 (tmtt)
REVERT: A   97 LEU cc_start: 0.8563 (mm) cc_final: 0.8361 (mm)
REVERT: A  158 PHE cc_start: 0.7614 (t80) cc_final: 0.7239 (t80)
REVERT: A  283 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7491 (mmt)
REVERT: A  317 ARG cc_start: 0.9302 (ttt180) cc_final: 0.8817 (ttp80)
REVERT: A  339 LEU cc_start: 0.8425 (mt) cc_final: 0.8176 (mt)
REVERT: A  518 MET cc_start: 0.8796 (mtm) cc_final: 0.8452 (mtm)
REVERT: A  556 MET cc_start: 0.8388 (mtp) cc_final: 0.8029 (mtp)
REVERT: A  589 PHE cc_start: 0.8610 (m-80) cc_final: 0.8239 (m-80)
  outliers start: 7
  outliers final: 3
  residues processed: 218
  average time/residue: 0.3464
  time to fit residues: 101.0973
Evaluate side-chains
  188 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 183
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 61 optimal weight:    5.9990
   chunk 55 optimal weight:    0.8980
   chunk 30 optimal weight:    5.9990
   chunk 18 optimal weight:    0.6980
   chunk 37 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 66 optimal weight:    5.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS
A 285 HIS
B  35 GLN
B 558 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.107145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.090927 restraints weight = 62030.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.095152 restraints weight = 32336.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.098123 restraints weight = 19846.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7009
moved from start:          0.3628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   5857  Z= 0.239
  Angle     :  0.813   8.295   7957  Z= 0.460
  Chirality :  0.045   0.173    943
  Planarity :  0.009   0.151    973
  Dihedral  :  7.795  31.106    787
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.50 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  3.41 %
    Favored  : 96.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

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: -1.62 (0.29), residues: 734
  helix: -0.72 (0.21), residues: 471
  sheet: -1.83 (0.83), residues: 40
  loop : -1.34 (0.42), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 553 
 HIS   0.006   0.002   HIS A  65 
 PHE   0.027   0.002   PHE A 361 
 TYR   0.035   0.003   TYR B 550 
 ARG   0.003   0.001   ARG B 549 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07185 (  366)
  hydrogen bonds       : angle       5.74350 ( 1068)
  SS BOND              : bond        0.00775 (    1)
  SS BOND              : angle       1.70621 (    2)
  covalent geometry    : bond        0.00469 ( 5856)
  covalent geometry    : angle       0.81225 ( 7955)

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 194
  time to evaluate  : 0.862 
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: 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: symmetry clash
   revert: symmetry clash
REVERT: A   27 ILE cc_start: 0.9559 (tp) cc_final: 0.9226 (tp)
REVERT: A  158 PHE cc_start: 0.7596 (t80) cc_final: 0.7198 (t80)
REVERT: A  235 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7745 (tm-30)
REVERT: A  258 LEU cc_start: 0.9185 (mt) cc_final: 0.8867 (mt)
REVERT: A  304 ASP cc_start: 0.9298 (m-30) cc_final: 0.8886 (m-30)
REVERT: A  518 MET cc_start: 0.9237 (mtm) cc_final: 0.8821 (mtm)
REVERT: A  527 PHE cc_start: 0.8721 (m-80) cc_final: 0.8131 (m-80)
REVERT: A  532 MET cc_start: 0.9256 (pmm) cc_final: 0.8454 (pmm)
REVERT: A  533 LEU cc_start: 0.8914 (mt) cc_final: 0.8450 (mt)
REVERT: B  505 ARG cc_start: 0.8837 (mmm160) cc_final: 0.8544 (mmp80)
  outliers start: 1
  outliers final: 1
  residues processed: 194
  average time/residue: 0.3415
  time to fit residues: 92.1488
Evaluate side-chains
  168 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 167
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 38 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 41 optimal weight:    0.5980
   chunk 48 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A   5 ASN
** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.106168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.090355 restraints weight = 62819.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.094634 restraints weight = 32535.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.097517 restraints weight = 19572.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7037
moved from start:          0.4493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5857  Z= 0.167
  Angle     :  0.703   7.178   7957  Z= 0.396
  Chirality :  0.041   0.161    943
  Planarity :  0.007   0.106    973
  Dihedral  :  7.129  29.919    787
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.09 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    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: -1.17 (0.29), residues: 734
  helix: -0.26 (0.22), residues: 465
  sheet: -1.46 (0.84), residues: 41
  loop : -1.46 (0.40), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 544 
 HIS   0.014   0.003   HIS A 285 
 PHE   0.021   0.002   PHE A  98 
 TYR   0.020   0.002   TYR B 550 
 ARG   0.004   0.001   ARG A  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06133 (  366)
  hydrogen bonds       : angle       5.29956 ( 1068)
  SS BOND              : bond        0.01872 (    1)
  SS BOND              : angle       5.00939 (    2)
  covalent geometry    : bond        0.00343 ( 5856)
  covalent geometry    : angle       0.69895 ( 7955)

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.862 
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: 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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LYS cc_start: 0.9476 (mttm) cc_final: 0.9029 (mmmt)
REVERT: A   53 MET cc_start: 0.8983 (mtm) cc_final: 0.8744 (ttt)
REVERT: A  128 LEU cc_start: 0.9169 (tp) cc_final: 0.8896 (tp)
REVERT: A  158 PHE cc_start: 0.7574 (t80) cc_final: 0.7213 (t80)
REVERT: A  204 MET cc_start: 0.8809 (mmm) cc_final: 0.8562 (mmm)
REVERT: A  214 LEU cc_start: 0.9191 (mp) cc_final: 0.8755 (mm)
REVERT: A  221 TYR cc_start: 0.8278 (t80) cc_final: 0.8012 (t80)
REVERT: A  235 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7789 (tm-30)
REVERT: A  258 LEU cc_start: 0.9018 (mt) cc_final: 0.8728 (mt)
REVERT: A  283 MET cc_start: 0.7244 (mmt) cc_final: 0.6945 (mmt)
REVERT: A  304 ASP cc_start: 0.9299 (m-30) cc_final: 0.8843 (m-30)
REVERT: A  316 MET cc_start: 0.8765 (mmm) cc_final: 0.8539 (mmm)
REVERT: A  317 ARG cc_start: 0.9440 (ttt180) cc_final: 0.9041 (ttp-170)
REVERT: A  405 GLN cc_start: 0.8969 (pt0) cc_final: 0.8448 (tm-30)
REVERT: A  518 MET cc_start: 0.9257 (mtm) cc_final: 0.8863 (mtm)
REVERT: A  527 PHE cc_start: 0.8691 (m-80) cc_final: 0.8391 (m-80)
REVERT: A  532 MET cc_start: 0.9198 (pmm) cc_final: 0.8374 (pmm)
REVERT: A  533 LEU cc_start: 0.8907 (mt) cc_final: 0.8398 (mt)
REVERT: A  589 PHE cc_start: 0.9234 (m-10) cc_final: 0.8975 (m-10)
REVERT: B  505 ARG cc_start: 0.8913 (mmm160) cc_final: 0.8576 (mmp80)
REVERT: B  544 TRP cc_start: 0.5943 (p-90) cc_final: 0.5489 (p-90)
  outliers start: 0
  outliers final: 0
  residues processed: 186
  average time/residue: 0.3132
  time to fit residues: 79.5943
Evaluate side-chains
  176 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 39 optimal weight:    0.8980
   chunk 36 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9980
   chunk 57 optimal weight:    0.5980
   chunk 20 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 69 optimal weight:    0.2980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 143 GLN ** 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 = 0.3662 r_free = 0.3662 target = 0.107108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.090842 restraints weight = 61482.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.095332 restraints weight = 31042.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.098370 restraints weight = 18389.110|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7040
moved from start:          0.5125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5857  Z= 0.145
  Angle     :  0.633   6.835   7957  Z= 0.351
  Chirality :  0.040   0.159    943
  Planarity :  0.007   0.108    973
  Dihedral  :  6.572  29.743    787
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.18 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    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: -0.66 (0.30), residues: 734
  helix:  0.19 (0.23), residues: 463
  sheet: -1.44 (0.87), residues: 41
  loop : -1.34 (0.41), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 544 
 HIS   0.007   0.002   HIS A 285 
 PHE   0.027   0.002   PHE A  96 
 TYR   0.030   0.002   TYR A 349 
 ARG   0.005   0.000   ARG B 536 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05097 (  366)
  hydrogen bonds       : angle       4.92061 ( 1068)
  SS BOND              : bond        0.00006 (    1)
  SS BOND              : angle       2.86955 (    2)
  covalent geometry    : bond        0.00301 ( 5856)
  covalent geometry    : angle       0.63150 ( 7955)

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 0.843 
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: 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: 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   45 LYS cc_start: 0.9489 (mttm) cc_final: 0.9060 (mmmt)
REVERT: A  158 PHE cc_start: 0.7732 (t80) cc_final: 0.7390 (t80)
REVERT: A  235 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7808 (tm-30)
REVERT: A  259 MET cc_start: 0.9050 (tpp) cc_final: 0.8202 (tpp)
REVERT: A  283 MET cc_start: 0.7282 (mmt) cc_final: 0.6938 (mmt)
REVERT: A  304 ASP cc_start: 0.9279 (m-30) cc_final: 0.8854 (m-30)
REVERT: A  317 ARG cc_start: 0.9539 (ttt180) cc_final: 0.9088 (ttp-170)
REVERT: A  330 THR cc_start: 0.9122 (t) cc_final: 0.8894 (t)
REVERT: A  338 PRO cc_start: 0.8776 (Cg_exo) cc_final: 0.8534 (Cg_endo)
REVERT: A  346 MET cc_start: 0.9522 (tpp) cc_final: 0.9017 (tmm)
REVERT: A  405 GLN cc_start: 0.9017 (pt0) cc_final: 0.8344 (tm-30)
REVERT: A  518 MET cc_start: 0.9294 (mtm) cc_final: 0.8915 (mtm)
REVERT: A  532 MET cc_start: 0.9094 (pmm) cc_final: 0.8179 (pmm)
REVERT: A  533 LEU cc_start: 0.8894 (mt) cc_final: 0.8357 (mt)
REVERT: A  550 MET cc_start: 0.8699 (tmm) cc_final: 0.8237 (tmm)
REVERT: A  589 PHE cc_start: 0.9214 (m-10) cc_final: 0.8949 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 195
  average time/residue: 0.3064
  time to fit residues: 81.9568
Evaluate side-chains
  178 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 46 optimal weight:    0.5980
   chunk 61 optimal weight:    0.8980
   chunk 18 optimal weight:    0.4980
   chunk 57 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 510 ASN ** 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 = 0.3623 r_free = 0.3623 target = 0.105130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.090103 restraints weight = 63619.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.094196 restraints weight = 34090.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.096978 restraints weight = 20906.293|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7153
moved from start:          0.5536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5857  Z= 0.160
  Angle     :  0.615   7.100   7957  Z= 0.343
  Chirality :  0.040   0.176    943
  Planarity :  0.006   0.080    973
  Dihedral  :  6.255  27.358    787
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.45 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    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: -0.56 (0.31), residues: 734
  helix:  0.29 (0.23), residues: 463
  sheet: -2.00 (0.80), residues: 44
  loop : -1.21 (0.42), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 553 
 HIS   0.005   0.001   HIS A 285 
 PHE   0.021   0.002   PHE A 603 
 TYR   0.019   0.002   TYR B 533 
 ARG   0.002   0.000   ARG B 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04743 (  366)
  hydrogen bonds       : angle       4.85363 ( 1068)
  SS BOND              : bond        0.00364 (    1)
  SS BOND              : angle       2.41594 (    2)
  covalent geometry    : bond        0.00318 ( 5856)
  covalent geometry    : angle       0.61381 ( 7955)

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 0.863 
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: 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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LYS cc_start: 0.9549 (mttm) cc_final: 0.9209 (mtpt)
REVERT: A  158 PHE cc_start: 0.7800 (t80) cc_final: 0.7464 (t80)
REVERT: A  259 MET cc_start: 0.9050 (tpp) cc_final: 0.8295 (tpp)
REVERT: A  304 ASP cc_start: 0.9212 (m-30) cc_final: 0.8901 (m-30)
REVERT: A  317 ARG cc_start: 0.9545 (ttt180) cc_final: 0.9083 (ttp-170)
REVERT: A  330 THR cc_start: 0.9195 (t) cc_final: 0.8951 (t)
REVERT: A  346 MET cc_start: 0.9541 (tpp) cc_final: 0.9022 (tmm)
REVERT: A  405 GLN cc_start: 0.9046 (pt0) cc_final: 0.8316 (tm-30)
REVERT: A  518 MET cc_start: 0.9240 (mtm) cc_final: 0.8865 (mtm)
REVERT: A  532 MET cc_start: 0.9050 (pmm) cc_final: 0.8154 (pmm)
REVERT: A  550 MET cc_start: 0.8733 (tmm) cc_final: 0.8245 (tmm)
REVERT: B  520 GLN cc_start: 0.7832 (tt0) cc_final: 0.7498 (tp-100)
  outliers start: 0
  outliers final: 0
  residues processed: 194
  average time/residue: 0.3334
  time to fit residues: 91.3552
Evaluate side-chains
  178 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 40 optimal weight:    0.0970
   chunk 70 optimal weight:    0.6980
   chunk 52 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A   5 ASN
A 100 HIS
** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 354 ASN
** A 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 539 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.104796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.089493 restraints weight = 63132.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.093608 restraints weight = 33030.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.096456 restraints weight = 20163.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7142
moved from start:          0.5908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5857  Z= 0.146
  Angle     :  0.610   7.724   7957  Z= 0.336
  Chirality :  0.039   0.174    943
  Planarity :  0.006   0.078    973
  Dihedral  :  6.068  30.782    787
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.31 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -0.45 (0.30), residues: 734
  helix:  0.41 (0.23), residues: 463
  sheet: -2.05 (0.77), residues: 44
  loop : -1.23 (0.41), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 553 
 HIS   0.004   0.002   HIS A 285 
 PHE   0.012   0.001   PHE A  16 
 TYR   0.041   0.002   TYR B 540 
 ARG   0.003   0.000   ARG B 549 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04526 (  366)
  hydrogen bonds       : angle       4.72850 ( 1068)
  SS BOND              : bond        0.00426 (    1)
  SS BOND              : angle       1.79700 (    2)
  covalent geometry    : bond        0.00301 ( 5856)
  covalent geometry    : angle       0.60957 ( 7955)

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.912 
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: 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   95 ILE cc_start: 0.8948 (mt) cc_final: 0.8568 (mt)
REVERT: A  158 PHE cc_start: 0.7790 (t80) cc_final: 0.7440 (t80)
REVERT: A  259 MET cc_start: 0.9056 (tpp) cc_final: 0.8307 (tpp)
REVERT: A  304 ASP cc_start: 0.9207 (m-30) cc_final: 0.8894 (m-30)
REVERT: A  316 MET cc_start: 0.9091 (mmm) cc_final: 0.8860 (mmm)
REVERT: A  317 ARG cc_start: 0.9524 (ttt180) cc_final: 0.9050 (ttp-170)
REVERT: A  330 THR cc_start: 0.9203 (t) cc_final: 0.8954 (t)
REVERT: A  405 GLN cc_start: 0.9065 (pt0) cc_final: 0.8297 (tm-30)
REVERT: A  471 MET cc_start: 0.8555 (tpp) cc_final: 0.8257 (tpp)
REVERT: A  518 MET cc_start: 0.9206 (mtm) cc_final: 0.8800 (mtm)
REVERT: A  532 MET cc_start: 0.9025 (pmm) cc_final: 0.8183 (pmm)
REVERT: A  550 MET cc_start: 0.8832 (tmm) cc_final: 0.8356 (tmm)
REVERT: B  520 GLN cc_start: 0.7804 (tt0) cc_final: 0.7432 (tp-100)
REVERT: B  546 ASN cc_start: 0.8701 (t0) cc_final: 0.8312 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 189
  average time/residue: 0.3004
  time to fit residues: 78.6459
Evaluate side-chains
  183 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 0.851 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   chunk 58 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   chunk 52 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 510 ASN ** 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 = 0.3629 r_free = 0.3629 target = 0.105098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.090113 restraints weight = 63946.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.094187 restraints weight = 33862.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.096963 restraints weight = 20774.773|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7163
moved from start:          0.6132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5857  Z= 0.147
  Angle     :  0.598   6.338   7957  Z= 0.332
  Chirality :  0.040   0.177    943
  Planarity :  0.006   0.078    973
  Dihedral  :  5.911  30.220    787
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.77 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -0.32 (0.30), residues: 734
  helix:  0.54 (0.23), residues: 463
  sheet: -2.02 (0.78), residues: 44
  loop : -1.24 (0.40), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 553 
 HIS   0.003   0.001   HIS A 285 
 PHE   0.017   0.001   PHE A 603 
 TYR   0.025   0.002   TYR A 349 
 ARG   0.002   0.000   ARG B 536 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04371 (  366)
  hydrogen bonds       : angle       4.66102 ( 1068)
  SS BOND              : bond        0.00303 (    1)
  SS BOND              : angle       1.79898 (    2)
  covalent geometry    : bond        0.00299 ( 5856)
  covalent geometry    : angle       0.59736 ( 7955)

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 0.884 
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: 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: symmetry clash
REVERT: A  158 PHE cc_start: 0.7817 (t80) cc_final: 0.7465 (t80)
REVERT: A  259 MET cc_start: 0.9045 (tpp) cc_final: 0.8392 (tpp)
REVERT: A  304 ASP cc_start: 0.9188 (m-30) cc_final: 0.8877 (m-30)
REVERT: A  316 MET cc_start: 0.9110 (mmm) cc_final: 0.8881 (mmm)
REVERT: A  317 ARG cc_start: 0.9517 (ttt180) cc_final: 0.9052 (ttp-170)
REVERT: A  330 THR cc_start: 0.9221 (t) cc_final: 0.8975 (t)
REVERT: A  405 GLN cc_start: 0.9177 (pt0) cc_final: 0.8244 (tm-30)
REVERT: A  518 MET cc_start: 0.9196 (mtm) cc_final: 0.8821 (mtm)
REVERT: A  532 MET cc_start: 0.8940 (pmm) cc_final: 0.8076 (pmm)
REVERT: A  550 MET cc_start: 0.8823 (tmm) cc_final: 0.8375 (tmm)
REVERT: A  556 MET cc_start: 0.8391 (mtp) cc_final: 0.8189 (mtp)
REVERT: B  520 GLN cc_start: 0.7750 (tt0) cc_final: 0.7396 (tp-100)
REVERT: B  546 ASN cc_start: 0.8709 (t0) cc_final: 0.8288 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 194
  average time/residue: 0.2942
  time to fit residues: 79.1470
Evaluate side-chains
  179 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 63 optimal weight:    0.0870
   chunk 61 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.7760

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

Flipped N/Q/H residues before XYZ refinement:
A   5 ASN
** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 510 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 = 0.3631 r_free = 0.3631 target = 0.105293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.090232 restraints weight = 64493.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.094307 restraints weight = 34122.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.097087 restraints weight = 20869.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7167
moved from start:          0.6365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5857  Z= 0.144
  Angle     :  0.593   6.376   7957  Z= 0.328
  Chirality :  0.039   0.184    943
  Planarity :  0.006   0.083    973
  Dihedral  :  5.849  30.725    787
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.63 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -0.11 (0.31), residues: 734
  helix:  0.71 (0.24), residues: 464
  sheet: -1.95 (0.78), residues: 44
  loop : -1.17 (0.41), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 553 
 HIS   0.004   0.001   HIS A 100 
 PHE   0.055   0.002   PHE A 361 
 TYR   0.018   0.002   TYR B 550 
 ARG   0.002   0.000   ARG B 536 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04217 (  366)
  hydrogen bonds       : angle       4.63426 ( 1068)
  SS BOND              : bond        0.00275 (    1)
  SS BOND              : angle       1.70120 (    2)
  covalent geometry    : bond        0.00294 ( 5856)
  covalent geometry    : angle       0.59249 ( 7955)

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.844 
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: 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   60 VAL cc_start: 0.9631 (t) cc_final: 0.9398 (p)
REVERT: A  158 PHE cc_start: 0.7989 (t80) cc_final: 0.7624 (t80)
REVERT: A  259 MET cc_start: 0.8931 (tpp) cc_final: 0.8320 (tpp)
REVERT: A  304 ASP cc_start: 0.9196 (m-30) cc_final: 0.8888 (m-30)
REVERT: A  316 MET cc_start: 0.9214 (mmm) cc_final: 0.8909 (mmm)
REVERT: A  317 ARG cc_start: 0.9518 (ttt180) cc_final: 0.9061 (ttp-170)
REVERT: A  330 THR cc_start: 0.9225 (t) cc_final: 0.8982 (t)
REVERT: A  405 GLN cc_start: 0.9199 (pt0) cc_final: 0.8268 (tm-30)
REVERT: A  471 MET cc_start: 0.8573 (tpp) cc_final: 0.8301 (tpp)
REVERT: A  518 MET cc_start: 0.9193 (mtm) cc_final: 0.8819 (mtm)
REVERT: A  532 MET cc_start: 0.8943 (pmm) cc_final: 0.8094 (pmm)
REVERT: A  550 MET cc_start: 0.8884 (tmm) cc_final: 0.8402 (tmm)
REVERT: B  520 GLN cc_start: 0.7611 (tt0) cc_final: 0.7248 (tp-100)
  outliers start: 0
  outliers final: 0
  residues processed: 189
  average time/residue: 0.3382
  time to fit residues: 88.1518
Evaluate side-chains
  182 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 41 optimal weight:    0.0870
   chunk 63 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 28 optimal weight:    4.9990
   chunk 46 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
** A 143 GLN ** 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 = 0.3649 r_free = 0.3649 target = 0.106202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.090872 restraints weight = 64617.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.094975 restraints weight = 34568.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.097860 restraints weight = 21289.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7156
moved from start:          0.6563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5857  Z= 0.125
  Angle     :  0.569   6.226   7957  Z= 0.311
  Chirality :  0.039   0.165    943
  Planarity :  0.006   0.087    973
  Dihedral  :  5.583  28.926    787
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.04 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    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:  0.18 (0.31), residues: 734
  helix:  0.99 (0.24), residues: 458
  sheet: -1.98 (0.77), residues: 44
  loop : -1.10 (0.41), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP A 227 
 HIS   0.004   0.001   HIS A 100 
 PHE   0.024   0.001   PHE A 361 
 TYR   0.018   0.002   TYR B 533 
 ARG   0.007   0.000   ARG B 549 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04005 (  366)
  hydrogen bonds       : angle       4.49184 ( 1068)
  SS BOND              : bond        0.00299 (    1)
  SS BOND              : angle       1.56789 (    2)
  covalent geometry    : bond        0.00262 ( 5856)
  covalent geometry    : angle       0.56811 ( 7955)

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 0.988 
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: 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: symmetry clash
REVERT: A   60 VAL cc_start: 0.9629 (t) cc_final: 0.9389 (p)
REVERT: A  136 MET cc_start: 0.9289 (mtp) cc_final: 0.9036 (mtp)
REVERT: A  158 PHE cc_start: 0.7968 (t80) cc_final: 0.7600 (t80)
REVERT: A  204 MET cc_start: 0.8844 (mmm) cc_final: 0.8642 (mmm)
REVERT: A  236 LYS cc_start: 0.8936 (ttmt) cc_final: 0.8381 (tppt)
REVERT: A  259 MET cc_start: 0.8886 (tpp) cc_final: 0.8205 (tpp)
REVERT: A  304 ASP cc_start: 0.9199 (m-30) cc_final: 0.8915 (m-30)
REVERT: A  317 ARG cc_start: 0.9509 (ttt180) cc_final: 0.9076 (ttp-170)
REVERT: A  329 ILE cc_start: 0.9405 (mm) cc_final: 0.8947 (tp)
REVERT: A  405 GLN cc_start: 0.9226 (pt0) cc_final: 0.8333 (tm-30)
REVERT: A  471 MET cc_start: 0.8595 (tpp) cc_final: 0.8269 (tpp)
REVERT: A  532 MET cc_start: 0.8928 (pmm) cc_final: 0.8092 (pmm)
REVERT: A  550 MET cc_start: 0.8884 (tmm) cc_final: 0.8380 (tmm)
REVERT: A  589 PHE cc_start: 0.9199 (m-10) cc_final: 0.8867 (m-80)
REVERT: B  520 GLN cc_start: 0.7580 (tt0) cc_final: 0.7201 (tp-100)
REVERT: B  546 ASN cc_start: 0.7410 (t0) cc_final: 0.7094 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 198
  average time/residue: 0.3647
  time to fit residues: 100.0939
Evaluate side-chains
  179 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 1.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 66 optimal weight:    6.9990
   chunk 27 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 24 optimal weight:    0.5980
   chunk 57 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0970
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
A   5 ASN
** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.105546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.089969 restraints weight = 63068.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.094146 restraints weight = 33676.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.097057 restraints weight = 20676.268|
|-----------------------------------------------------------------------------|
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7169
moved from start:          0.6820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5857  Z= 0.131
  Angle     :  0.559   5.991   7957  Z= 0.308
  Chirality :  0.039   0.163    943
  Planarity :  0.005   0.080    973
  Dihedral  :  5.522  28.833    787
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.90 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    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:  0.33 (0.31), residues: 734
  helix:  1.07 (0.24), residues: 462
  sheet: -1.98 (0.76), residues: 44
  loop : -0.97 (0.42), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 227 
 HIS   0.003   0.001   HIS A 100 
 PHE   0.026   0.001   PHE A 361 
 TYR   0.016   0.002   TYR B 533 
 ARG   0.006   0.000   ARG A 226 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03897 (  366)
  hydrogen bonds       : angle       4.43103 ( 1068)
  SS BOND              : bond        0.00272 (    1)
  SS BOND              : angle       1.53330 (    2)
  covalent geometry    : bond        0.00272 ( 5856)
  covalent geometry    : angle       0.55894 ( 7955)

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 0.964 
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: 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: symmetry clash
REVERT: A   60 VAL cc_start: 0.9632 (t) cc_final: 0.9418 (p)
REVERT: A  158 PHE cc_start: 0.7984 (t80) cc_final: 0.7611 (t80)
REVERT: A  236 LYS cc_start: 0.8934 (ttmt) cc_final: 0.8366 (tppt)
REVERT: A  259 MET cc_start: 0.8909 (tpp) cc_final: 0.7985 (tpp)
REVERT: A  304 ASP cc_start: 0.9202 (m-30) cc_final: 0.8947 (m-30)
REVERT: A  317 ARG cc_start: 0.9495 (ttt180) cc_final: 0.9053 (ttp-170)
REVERT: A  329 ILE cc_start: 0.9401 (mm) cc_final: 0.8949 (tp)
REVERT: A  405 GLN cc_start: 0.9326 (pt0) cc_final: 0.8337 (tm-30)
REVERT: A  532 MET cc_start: 0.8930 (pmm) cc_final: 0.8136 (pmm)
REVERT: A  550 MET cc_start: 0.8893 (tmm) cc_final: 0.8427 (tmm)
REVERT: A  589 PHE cc_start: 0.9191 (m-10) cc_final: 0.8843 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 190
  average time/residue: 0.3294
  time to fit residues: 85.8889
Evaluate side-chains
  175 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 59 optimal weight:    0.4980
   chunk 2 optimal weight:    0.0980
   chunk 66 optimal weight:    0.0970
   chunk 42 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 43 optimal weight:    0.5980
   chunk 46 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 17 optimal weight:    0.4980
   chunk 12 optimal weight:    0.0030
   overall best weight:    0.2388

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

Flipped N/Q/H residues before XYZ refinement:
** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 539 GLN ** 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 = 0.3658 r_free = 0.3658 target = 0.106780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.091236 restraints weight = 61154.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.095568 restraints weight = 31805.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.098472 restraints weight = 19136.163|
|-----------------------------------------------------------------------------|
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7108
moved from start:          0.6992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   5857  Z= 0.114
  Angle     :  0.556   6.710   7957  Z= 0.298
  Chirality :  0.039   0.161    943
  Planarity :  0.005   0.080    973
  Dihedral  :  5.300  27.420    787
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.90 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    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:  0.61 (0.32), residues: 734
  helix:  1.32 (0.24), residues: 457
  sheet: -1.92 (0.76), residues: 44
  loop : -0.89 (0.43), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 553 
 HIS   0.004   0.001   HIS A 100 
 PHE   0.018   0.001   PHE A 603 
 TYR   0.017   0.002   TYR B 533 
 ARG   0.009   0.001   ARG B 549 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03765 (  366)
  hydrogen bonds       : angle       4.26682 ( 1068)
  SS BOND              : bond        0.00295 (    1)
  SS BOND              : angle       1.49299 (    2)
  covalent geometry    : bond        0.00247 ( 5856)
  covalent geometry    : angle       0.55571 ( 7955)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4596.86 seconds
wall clock time: 80 minutes 6.96 seconds (4806.96 seconds total)