Starting phenix.real_space_refine
on Tue Apr 29 19:15:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fuz_50783/04_2025/9fuz_50783.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fuz_50783/04_2025/9fuz_50783.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fuz_50783/04_2025/9fuz_50783.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fuz_50783/04_2025/9fuz_50783.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fuz_50783/04_2025/9fuz_50783.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fuz_50783/04_2025/9fuz_50783.cif"
  }
  resolution = 4.2
  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=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      54      5.16       5
     C    5590      2.51       5
     N    1536      2.21       5
     O    1642      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 8822
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 4411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 569, 4411
          Classifications: {'peptide': 569}
          Link IDs: {'PTRANS': 13, 'TRANS': 555}
    Chain: "A"
      Number of atoms: 4411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 569, 4411
          Classifications: {'peptide': 569}
          Link IDs: {'PTRANS': 13, 'TRANS': 555}
  Time building chain proxies: 6.31, per 1000 atoms: 0.72
  Number of scatterers: 8822
  At special positions: 0
  Unit cell: (113.56, 115.6, 135.32, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      54     16.00
     O    1642      8.00
     N    1536      7.00
     C    5590      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.24
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2128

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 5 sheets defined
      68.8% alpha, 4.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.81
  Creating SS restraints...
    Processing helix  chain 'B' and resid 16 through 21
      removed outlier: 3.752A  pdb=" N   ILE B  20 " --> pdb=" O   LEU B  16 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 23 through 54
      removed outlier: 3.542A  pdb=" N   LEU B  27 " --> pdb=" O   PHE B  23 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   LYS B  49 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
      Proline residue:  B  50  - end of helix
    Processing helix  chain 'B' and resid 61 through 111
      removed outlier: 3.598A  pdb=" N   TRP B  66 " --> pdb=" O   SER B  62 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   MET B  67 " --> pdb=" O   VAL B  63 " (cutoff:3.500A)
      Proline residue:  B  68  - end of helix
      removed outlier: 3.660A  pdb=" N   GLY B 110 " --> pdb=" O   GLY B 106 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 117
      removed outlier: 3.722A  pdb=" N   PHE B 116 " --> pdb=" O   PRO B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 164
      removed outlier: 3.819A  pdb=" N   ASP B 131 " --> pdb=" O   ARG B 127 " (cutoff:3.500A)
      removed outlier: 5.004A  pdb=" N   SER B 132 " --> pdb=" O   ILE B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 213
      removed outlier: 3.773A  pdb=" N   SER B 168 " --> pdb=" O   SER B 164 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ILE B 169 " --> pdb=" O   TRP B 165 " (cutoff:3.500A)
      Proline residue:  B 176  - end of helix
      removed outlier: 4.557A  pdb=" N   GLY B 213 " --> pdb=" O   GLN B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 221
    Processing helix  chain 'B' and resid 222 through 272
      removed outlier: 3.569A  pdb=" N   SER B 251 " --> pdb=" O   ALA B 247 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   ASP B 252 " --> pdb=" O   SER B 248 " (cutoff:3.500A)
      Proline residue:  B 253  - end of helix
    Processing helix  chain 'B' and resid 282 through 303
      removed outlier: 4.000A  pdb=" N   ARG B 296 " --> pdb=" O   ILE B 292 " (cutoff:3.500A)
      Proline residue:  B 297  - end of helix
      removed outlier: 3.592A  pdb=" N   THR B 302 " --> pdb=" O   LEU B 298 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   ASN B 303 " --> pdb=" O   LYS B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 303 through 323
      removed outlier: 3.667A  pdb=" N   ILE B 321 " --> pdb=" O   THR B 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 390
      removed outlier: 3.748A  pdb=" N   ILE B 389 " --> pdb=" O   ILE B 385 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   THR B 390 " --> pdb=" O   ALA B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 418
    Processing helix  chain 'B' and resid 432 through 438
    Processing helix  chain 'B' and resid 446 through 458
    Processing helix  chain 'B' and resid 459 through 464
    Processing helix  chain 'B' and resid 482 through 498
    Processing helix  chain 'B' and resid 515 through 528
    Processing helix  chain 'B' and resid 538 through 545
    Processing helix  chain 'B' and resid 561 through 568
    Processing helix  chain 'B' and resid 571 through 580
      removed outlier: 3.656A  pdb=" N   MET B 578 " --> pdb=" O   GLN B 574 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 16 through 21
    Processing helix  chain 'A' and resid 23 through 47
      removed outlier: 3.682A  pdb=" N   ALA A  33 " --> pdb=" O   VAL A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 54
    Processing helix  chain 'A' and resid 62 through 109
      Proline residue:  A  68  - end of helix
      removed outlier: 4.039A  pdb=" N   ILE A  72 " --> pdb=" O   PRO A  68 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   GLY A  73 " --> pdb=" O   LEU A  69 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   LYS A  95 " --> pdb=" O   TRP A  91 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   MET A 100 " --> pdb=" O   VAL A  96 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   HIS A 107 " --> pdb=" O   ARG A 103 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   MET A 108 " --> pdb=" O   LEU A 104 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   MET A 109 " --> pdb=" O   PHE A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 117
      removed outlier: 4.402A  pdb=" N   PHE A 116 " --> pdb=" O   PRO A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 163
      removed outlier: 3.627A  pdb=" N   SER A 126 " --> pdb=" O   GLY A 122 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   TYR A 130 " --> pdb=" O   SER A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 213
      removed outlier: 3.655A  pdb=" N   ALA A 175 " --> pdb=" O   LEU A 171 " (cutoff:3.500A)
      Proline residue:  A 176  - end of helix
      removed outlier: 3.661A  pdb=" N   GLN A 209 " --> pdb=" O   THR A 205 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   MET A 210 " --> pdb=" O   SER A 206 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   LEU A 211 " --> pdb=" O   ALA A 207 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   GLY A 213 " --> pdb=" O   GLN A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 221
    Processing helix  chain 'A' and resid 222 through 270
      removed outlier: 3.958A  pdb=" N   ASP A 252 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
      Proline residue:  A 253  - end of helix
      removed outlier: 4.053A  pdb=" N   ALA A 270 " --> pdb=" O   VAL A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 276
      removed outlier: 6.642A  pdb=" N   SER A 274 " --> pdb=" O   SER A 271 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   VAL A 275 " --> pdb=" O   PHE A 272 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   MET A 276 " --> pdb=" O   PRO A 273 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 271 through 276'
    Processing helix  chain 'A' and resid 283 through 302
      removed outlier: 3.514A  pdb=" N   MET A 291 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ARG A 296 " --> pdb=" O   ILE A 292 " (cutoff:3.500A)
      Proline residue:  A 297  - end of helix
      removed outlier: 3.621A  pdb=" N   SER A 300 " --> pdb=" O   ARG A 296 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   THR A 302 " --> pdb=" O   LEU A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 324
      removed outlier: 3.687A  pdb=" N   ARG A 310 " --> pdb=" O   ALA A 306 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ILE A 321 " --> pdb=" O   THR A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 391
      removed outlier: 4.471A  pdb=" N   ALA A 386 " --> pdb=" O   LYS A 382 " (cutoff:3.500A)
      removed outlier: 5.458A  pdb=" N   SER A 387 " --> pdb=" O   SER A 383 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ILE A 389 " --> pdb=" O   ILE A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 418
    Processing helix  chain 'A' and resid 432 through 438
      removed outlier: 3.762A  pdb=" N   ALA A 438 " --> pdb=" O   ALA A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 457
    Processing helix  chain 'A' and resid 459 through 466
    Processing helix  chain 'A' and resid 482 through 498
    Processing helix  chain 'A' and resid 515 through 529
      removed outlier: 4.165A  pdb=" N   ASN A 529 " --> pdb=" O   GLU A 525 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 544
    Processing helix  chain 'A' and resid 561 through 568
    Processing helix  chain 'A' and resid 571 through 579
    Processing sheet with id=AA1, first strand: chain 'B' and resid 359 through 362
      removed outlier: 3.511A  pdb=" N   ASN B 361 " --> pdb=" O   VAL B 347 " (cutoff:3.500A)
      removed outlier: 5.313A  pdb=" N   VAL B 347 " --> pdb=" O   ASN B 361 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   VAL B 347 " --> pdb=" O   GLU B 397 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   GLU B 397 " --> pdb=" O   VAL B 347 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 419 through 422
      removed outlier: 6.733A  pdb=" N   LEU B 502 " --> pdb=" O   LEU B 533 " (cutoff:3.500A)
      removed outlier: 7.578A  pdb=" N   ILE B 535 " --> pdb=" O   LEU B 502 " (cutoff:3.500A)
      removed outlier: 5.948A  pdb=" N   LEU B 504 " --> pdb=" O   ILE B 535 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   VAL B 372 " --> pdb=" O   VAL B 534 " (cutoff:3.500A)
      removed outlier: 6.121A  pdb=" N   ALA B 373 " --> pdb=" O   VAL B 549 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 342 through 343
    Processing sheet with id=AA4, first strand: chain 'A' and resid 419 through 421
      removed outlier: 6.428A  pdb=" N   VAL A 372 " --> pdb=" O   VAL A 534 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   THR A 371 " --> pdb=" O   GLU A 547 " (cutoff:3.500A)
      removed outlier: 7.959A  pdb=" N   VAL A 549 " --> pdb=" O   THR A 371 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   ALA A 373 " --> pdb=" O   VAL A 549 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   VAL A 551 " --> pdb=" O   ALA A 373 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   ILE A 548 " --> pdb=" O   ARG A 559 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   ARG A 559 " --> pdb=" O   ILE A 548 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   VAL A 550 " --> pdb=" O   VAL A 557 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 401 through 402

    557 hydrogen bonds defined for protein.
    1656 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.51

  Time building geometry restraints manager: 2.65 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2306
        1.33 -     1.46: 1566
        1.46 -     1.58: 4974
        1.58 -     1.70: 0
        1.70 -     1.82: 104
  Bond restraints: 8950
  Sorted by residual:
  bond pdb=" N   ASP A 252 "
       pdb=" CA  ASP A 252 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 9.20e-03 1.18e+04 1.22e+01
  bond pdb=" N   VAL B 245 "
       pdb=" CA  VAL B 245 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.034 1.23e-02 6.61e+03 7.78e+00
  bond pdb=" N   MET A 111 "
       pdb=" CA  MET A 111 "
    ideal  model  delta    sigma   weight residual
    1.453  1.493 -0.040 1.44e-02 4.82e+03 7.61e+00
  bond pdb=" N   SER A 251 "
       pdb=" CA  SER A 251 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.17e-02 7.31e+03 6.63e+00
  bond pdb=" N   MET B 244 "
       pdb=" CA  MET B 244 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.21e-02 6.83e+03 6.54e+00
  ... (remaining 8945 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.32: 11642
        2.32 -     4.65: 378
        4.65 -     6.97: 56
        6.97 -     9.29: 12
        9.29 -    11.61: 4
  Bond angle restraints: 12092
  Sorted by residual:
  angle pdb=" CA  GLU B 208 "
        pdb=" CB  GLU B 208 "
        pdb=" CG  GLU B 208 "
      ideal   model   delta    sigma   weight residual
     114.10  123.55   -9.45 2.00e+00 2.50e-01 2.23e+01
  angle pdb=" N   GLU B 208 "
        pdb=" CA  GLU B 208 "
        pdb=" CB  GLU B 208 "
      ideal   model   delta    sigma   weight residual
     110.12  116.30   -6.18 1.47e+00 4.63e-01 1.77e+01
  angle pdb=" CB  MET A 244 "
        pdb=" CG  MET A 244 "
        pdb=" SD  MET A 244 "
      ideal   model   delta    sigma   weight residual
     112.70  124.31  -11.61 3.00e+00 1.11e-01 1.50e+01
  angle pdb=" CB  MET A 200 "
        pdb=" CG  MET A 200 "
        pdb=" SD  MET A 200 "
      ideal   model   delta    sigma   weight residual
     112.70  124.03  -11.33 3.00e+00 1.11e-01 1.43e+01
  angle pdb=" CB  MET B 200 "
        pdb=" CG  MET B 200 "
        pdb=" SD  MET B 200 "
      ideal   model   delta    sigma   weight residual
     112.70  123.59  -10.89 3.00e+00 1.11e-01 1.32e+01
  ... (remaining 12087 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.19: 4660
       17.19 -    34.38: 594
       34.38 -    51.58: 160
       51.58 -    68.77: 30
       68.77 -    85.96: 10
  Dihedral angle restraints: 5454
    sinusoidal: 2164
      harmonic: 3290
  Sorted by residual:
  dihedral pdb=" CA  ARG A  14 "
           pdb=" C   ARG A  14 "
           pdb=" N   ARG A  15 "
           pdb=" CA  ARG A  15 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.05   21.95     0      5.00e+00 4.00e-02 1.93e+01
  dihedral pdb=" CA  ARG A 391 "
           pdb=" C   ARG A 391 "
           pdb=" N   PHE A 392 "
           pdb=" CA  PHE A 392 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.56   21.44     0      5.00e+00 4.00e-02 1.84e+01
  dihedral pdb=" CA  ALA B 536 "
           pdb=" C   ALA B 536 "
           pdb=" N   HIS B 537 "
           pdb=" CA  HIS B 537 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.63   20.37     0      5.00e+00 4.00e-02 1.66e+01
  ... (remaining 5451 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 1188
       0.059 -    0.117: 217
       0.117 -    0.176: 29
       0.176 -    0.235: 5
       0.235 -    0.293: 1
  Chirality restraints: 1440
  Sorted by residual:
  chirality pdb=" CB  VAL B  96 "
            pdb=" CA  VAL B  96 "
            pdb=" CG1 VAL B  96 "
            pdb=" CG2 VAL B  96 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.34   -0.29 2.00e-01 2.50e+01 2.15e+00
  chirality pdb=" CG  LEU B  34 "
            pdb=" CB  LEU B  34 "
            pdb=" CD1 LEU B  34 "
            pdb=" CD2 LEU B  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.37   -0.21 2.00e-01 2.50e+01 1.15e+00
  chirality pdb=" CA  GLU B 226 "
            pdb=" N   GLU B 226 "
            pdb=" C   GLU B 226 "
            pdb=" CB  GLU B 226 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.12e+00
  ... (remaining 1437 not shown)

  Planarity restraints: 1532
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 272 "    0.051 5.00e-02 4.00e+02   7.67e-02 9.40e+00
        pdb=" N   PRO A 273 "   -0.133 5.00e-02 4.00e+02
        pdb=" CA  PRO A 273 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 273 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 250 "    0.011 2.00e-02 2.50e+03   2.24e-02 5.03e+00
        pdb=" C   ILE A 250 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   ILE A 250 "    0.015 2.00e-02 2.50e+03
        pdb=" N   SER A 251 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 311 "   -0.011 2.00e-02 2.50e+03   2.20e-02 4.83e+00
        pdb=" C   GLY A 311 "    0.038 2.00e-02 2.50e+03
        pdb=" O   GLY A 311 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   MET A 312 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1529 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 898
        2.74 -     3.28: 10125
        3.28 -     3.82: 15103
        3.82 -     4.36: 17336
        4.36 -     4.90: 27646
  Nonbonded interactions: 71108
  Sorted by model distance:
  nonbonded pdb=" O   LEU A  16 "
            pdb=" OG1 THR A  19 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" O   ILE A 128 "
            pdb=" OG  SER A 132 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" O   PRO B 176 "
            pdb=" OG  SER B 179 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" O   TRP A 165 "
            pdb=" OG  SER A 168 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" O   SER B  86 "
            pdb=" OG  SER B  90 "
     model   vdw
     2.253 3.040
  ... (remaining 71103 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.460
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     23.500
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
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      :  0.005   0.069   8950  Z= 0.246
  Angle     :  0.982  11.614  12092  Z= 0.528
  Chirality :  0.047   0.293   1440
  Planarity :  0.006   0.077   1532
  Dihedral  : 16.668  85.961   3326
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.59 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 28.51 %
    Favored  : 70.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.25 (0.24), residues: 1134
  helix:  0.48 (0.18), residues: 724
  sheet: -0.33 (0.87), residues: 36
  loop : -1.31 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A  66 
 HIS   0.012   0.002   HIS A 214 
 PHE   0.032   0.002   PHE A 115 
 TYR   0.013   0.001   TYR B 163 
 ARG   0.011   0.001   ARG A 488 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14856 (  557)
  hydrogen bonds       : angle       7.12758 ( 1656)
  covalent geometry    : bond        0.00509 ( 8950)
  covalent geometry    : angle       0.98206 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 227
  time to evaluate  : 0.998 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   98 MET cc_start: 0.9331 (ttt) cc_final: 0.8850 (tpp)
REVERT: B  115 PHE cc_start: 0.9394 (t80) cc_final: 0.9105 (t80)
REVERT: B  210 MET cc_start: 0.8211 (tpp) cc_final: 0.7999 (tpp)
REVERT: B  242 MET cc_start: 0.9122 (mmm) cc_final: 0.8896 (mmm)
REVERT: B  244 MET cc_start: 0.9371 (ppp) cc_final: 0.9009 (ppp)
REVERT: B  255 ILE cc_start: 0.9590 (mp) cc_final: 0.9335 (tp)
REVERT: B  360 ARG cc_start: 0.9495 (ttt180) cc_final: 0.9281 (mmm160)
REVERT: A  109 MET cc_start: 0.8577 (mmp) cc_final: 0.7501 (tmm)
REVERT: A  226 GLU cc_start: 0.9280 (tp30) cc_final: 0.8985 (tp30)
REVERT: A  276 MET cc_start: 0.8065 (mmt) cc_final: 0.7818 (mmm)
REVERT: A  402 MET cc_start: 0.9444 (tmm) cc_final: 0.9160 (tmm)
REVERT: A  410 TYR cc_start: 0.8721 (m-80) cc_final: 0.8436 (t80)
REVERT: A  538 ARG cc_start: 0.8180 (tpp-160) cc_final: 0.7929 (tpp-160)
  outliers start: 6
  outliers final: 2
  residues processed: 228
  average time/residue: 0.1836
  time to fit residues: 60.1359
Evaluate side-chains
  211 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 209
  time to evaluate  : 1.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    3.9990
   chunk 84 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 87 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 53 optimal weight:   10.0000
   chunk 65 optimal weight:    0.9990
   chunk 101 optimal weight:    3.9990
   overall best weight:    1.5990

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

Flipped N/Q/H residues before XYZ refinement:
B 256 GLN
A 134 GLN
A 537 HIS
A 574 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.076503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.056196 restraints weight = 33680.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.058423 restraints weight = 20696.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.060083 restraints weight = 14583.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.2351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   8950  Z= 0.180
  Angle     :  0.641   9.265  12092  Z= 0.348
  Chirality :  0.043   0.218   1440
  Planarity :  0.004   0.062   1532
  Dihedral  :  4.936  20.210   1238
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.38 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  4.03 %
    Favored  : 95.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.45 (0.25), residues: 1134
  helix:  1.13 (0.18), residues: 730
  sheet: -0.93 (0.72), residues: 48
  loop : -1.21 (0.34), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 165 
 HIS   0.004   0.001   HIS B 214 
 PHE   0.023   0.002   PHE B 157 
 TYR   0.016   0.002   TYR A 572 
 ARG   0.003   0.000   ARG B  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05368 (  557)
  hydrogen bonds       : angle       5.17486 ( 1656)
  covalent geometry    : bond        0.00364 ( 8950)
  covalent geometry    : angle       0.64147 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 248
  time to evaluate  : 0.965 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   98 MET cc_start: 0.9364 (ttt) cc_final: 0.9014 (ttt)
REVERT: B  100 MET cc_start: 0.9601 (ttp) cc_final: 0.9325 (tmm)
REVERT: B  115 PHE cc_start: 0.9421 (t80) cc_final: 0.8954 (t80)
REVERT: B  200 MET cc_start: 0.9301 (tmm) cc_final: 0.8954 (tmm)
REVERT: B  226 GLU cc_start: 0.9385 (tp30) cc_final: 0.9147 (tp30)
REVERT: B  242 MET cc_start: 0.9112 (mmm) cc_final: 0.8845 (mmm)
REVERT: B  244 MET cc_start: 0.9268 (ppp) cc_final: 0.8990 (ppp)
REVERT: B  332 LYS cc_start: 0.9661 (mttt) cc_final: 0.9374 (mmtt)
REVERT: B  359 LEU cc_start: 0.9611 (tp) cc_final: 0.9349 (tp)
REVERT: B  360 ARG cc_start: 0.9585 (ttt180) cc_final: 0.9374 (mmm160)
REVERT: B  527 GLN cc_start: 0.9339 (pt0) cc_final: 0.9114 (pp30)
REVERT: A   98 MET cc_start: 0.9241 (ttm) cc_final: 0.8848 (ttt)
REVERT: A  109 MET cc_start: 0.8668 (mmp) cc_final: 0.8165 (tmm)
REVERT: A  149 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8627 (mm-30)
REVERT: A  160 MET cc_start: 0.9356 (mmm) cc_final: 0.9035 (mmm)
REVERT: A  200 MET cc_start: 0.9454 (tmm) cc_final: 0.9197 (tmm)
REVERT: A  210 MET cc_start: 0.8800 (mmt) cc_final: 0.8438 (mmm)
REVERT: A  226 GLU cc_start: 0.9332 (tp30) cc_final: 0.9129 (tp30)
REVERT: A  244 MET cc_start: 0.9374 (ppp) cc_final: 0.9086 (ppp)
REVERT: A  291 MET cc_start: 0.9604 (tpp) cc_final: 0.9353 (tpt)
REVERT: A  390 THR cc_start: 0.9207 (p) cc_final: 0.8994 (p)
REVERT: A  456 MET cc_start: 0.9152 (mmp) cc_final: 0.8934 (mmm)
REVERT: A  538 ARG cc_start: 0.8360 (tpp-160) cc_final: 0.8155 (tpm170)
  outliers start: 1
  outliers final: 0
  residues processed: 248
  average time/residue: 0.1694
  time to fit residues: 61.7740
Evaluate side-chains
  204 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 12 optimal weight:    0.7980
   chunk 79 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 52 optimal weight:   20.0000
   chunk 16 optimal weight:    0.9990
   chunk 48 optimal weight:    6.9990
   chunk 82 optimal weight:   20.0000
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
B 209 GLN
B 214 HIS
A 214 HIS
A 537 HIS
A 574 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.077064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.056910 restraints weight = 33745.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.059213 restraints weight = 20955.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.060908 restraints weight = 14784.930|
|-----------------------------------------------------------------------------|
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.2947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8950  Z= 0.140
  Angle     :  0.593   7.002  12092  Z= 0.318
  Chirality :  0.042   0.191   1440
  Planarity :  0.005   0.113   1532
  Dihedral  :  4.794  21.050   1238
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.20 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  3.82 %
    Favored  : 95.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.25), residues: 1134
  helix:  1.28 (0.19), residues: 724
  sheet:  0.24 (0.87), residues: 32
  loop : -1.30 (0.33), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  66 
 HIS   0.006   0.001   HIS B 576 
 PHE   0.016   0.002   PHE A 392 
 TYR   0.014   0.001   TYR B 410 
 ARG   0.006   0.000   ARG A 530 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04698 (  557)
  hydrogen bonds       : angle       4.88142 ( 1656)
  covalent geometry    : bond        0.00285 ( 8950)
  covalent geometry    : angle       0.59302 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 253
  time to evaluate  : 0.961 
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: B   47 LEU cc_start: 0.9102 (mt) cc_final: 0.8898 (mt)
REVERT: B   98 MET cc_start: 0.9380 (ttt) cc_final: 0.9042 (ttt)
REVERT: B  100 MET cc_start: 0.9578 (ttp) cc_final: 0.9301 (tmm)
REVERT: B  116 PHE cc_start: 0.9279 (m-80) cc_final: 0.9020 (m-10)
REVERT: B  156 LEU cc_start: 0.9654 (mt) cc_final: 0.9440 (mt)
REVERT: B  160 MET cc_start: 0.9384 (mtm) cc_final: 0.8990 (mtm)
REVERT: B  200 MET cc_start: 0.9366 (tmm) cc_final: 0.9001 (tmm)
REVERT: B  242 MET cc_start: 0.9113 (mmm) cc_final: 0.8882 (mmm)
REVERT: B  244 MET cc_start: 0.9287 (ppp) cc_final: 0.8938 (ppp)
REVERT: B  359 LEU cc_start: 0.9585 (tp) cc_final: 0.9337 (tp)
REVERT: B  360 ARG cc_start: 0.9597 (ttt180) cc_final: 0.9382 (mmm160)
REVERT: B  527 GLN cc_start: 0.9361 (pt0) cc_final: 0.9113 (pp30)
REVERT: B  538 ARG cc_start: 0.8335 (tpm170) cc_final: 0.8115 (tpp-160)
REVERT: A   98 MET cc_start: 0.9208 (ttm) cc_final: 0.8994 (ttt)
REVERT: A  109 MET cc_start: 0.8862 (mmp) cc_final: 0.8302 (tmm)
REVERT: A  115 PHE cc_start: 0.9003 (t80) cc_final: 0.8354 (t80)
REVERT: A  116 PHE cc_start: 0.8957 (m-80) cc_final: 0.8517 (m-80)
REVERT: A  149 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8648 (mm-30)
REVERT: A  160 MET cc_start: 0.9362 (mmm) cc_final: 0.9013 (mmm)
REVERT: A  200 MET cc_start: 0.9438 (tmm) cc_final: 0.9152 (tmm)
REVERT: A  210 MET cc_start: 0.8725 (mmt) cc_final: 0.8284 (mmm)
REVERT: A  244 MET cc_start: 0.9362 (ppp) cc_final: 0.9155 (ppp)
REVERT: A  295 MET cc_start: 0.8352 (ttt) cc_final: 0.8150 (ttt)
REVERT: A  315 CYS cc_start: 0.8909 (t) cc_final: 0.8702 (t)
  outliers start: 2
  outliers final: 0
  residues processed: 254
  average time/residue: 0.1754
  time to fit residues: 63.1863
Evaluate side-chains
  210 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 1.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 87 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 23 optimal weight:    7.9990
   chunk 98 optimal weight:    0.9990
   chunk 39 optimal weight:    5.9990
   chunk 16 optimal weight:    0.6980
   chunk 92 optimal weight:    0.9980
   chunk 99 optimal weight:    0.8980
   chunk 107 optimal weight:    5.9990
   chunk 2 optimal weight:    0.8980
   chunk 77 optimal weight:    0.0170
   overall best weight:    0.7018

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

Flipped N/Q/H residues before XYZ refinement:
** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 537 HIS
A 574 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.077739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.057317 restraints weight = 33140.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.059609 restraints weight = 20457.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.061320 restraints weight = 14446.116|
|-----------------------------------------------------------------------------|
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.3314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8950  Z= 0.130
  Angle     :  0.585   6.741  12092  Z= 0.311
  Chirality :  0.042   0.218   1440
  Planarity :  0.004   0.050   1532
  Dihedral  :  4.670  19.519   1238
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.85 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.10 %
    Favored  : 96.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.83 (0.25), residues: 1134
  helix:  1.43 (0.19), residues: 720
  sheet:  0.35 (0.87), residues: 32
  loop : -1.13 (0.33), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  66 
 HIS   0.004   0.001   HIS B 214 
 PHE   0.012   0.002   PHE B 288 
 TYR   0.016   0.001   TYR B 410 
 ARG   0.006   0.000   ARG B 236 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04432 (  557)
  hydrogen bonds       : angle       4.71129 ( 1656)
  covalent geometry    : bond        0.00269 ( 8950)
  covalent geometry    : angle       0.58464 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 253
  time to evaluate  : 1.038 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   98 MET cc_start: 0.9366 (ttt) cc_final: 0.8992 (ttt)
REVERT: B  100 MET cc_start: 0.9566 (ttp) cc_final: 0.9312 (tmm)
REVERT: B  108 MET cc_start: 0.9488 (mtp) cc_final: 0.9161 (mtp)
REVERT: B  111 MET cc_start: 0.9453 (ttt) cc_final: 0.9198 (tmm)
REVERT: B  149 GLU cc_start: 0.9034 (mp0) cc_final: 0.8693 (mp0)
REVERT: B  156 LEU cc_start: 0.9609 (mt) cc_final: 0.9406 (mt)
REVERT: B  160 MET cc_start: 0.9425 (mtm) cc_final: 0.9036 (mtm)
REVERT: B  200 MET cc_start: 0.9373 (tmm) cc_final: 0.8999 (tmm)
REVERT: B  208 GLU cc_start: 0.9102 (mp0) cc_final: 0.8878 (mt-10)
REVERT: B  237 MET cc_start: 0.9130 (ttp) cc_final: 0.8620 (ptm)
REVERT: B  242 MET cc_start: 0.9084 (mmm) cc_final: 0.8832 (mmm)
REVERT: B  244 MET cc_start: 0.9286 (ppp) cc_final: 0.8925 (ppp)
REVERT: B  527 GLN cc_start: 0.9356 (pt0) cc_final: 0.9118 (pp30)
REVERT: B  538 ARG cc_start: 0.8364 (tpm170) cc_final: 0.8130 (tpp-160)
REVERT: A  109 MET cc_start: 0.8501 (mmp) cc_final: 0.8148 (tmm)
REVERT: A  111 MET cc_start: 0.9081 (tmm) cc_final: 0.8746 (tmm)
REVERT: A  116 PHE cc_start: 0.8973 (m-80) cc_final: 0.8433 (m-80)
REVERT: A  121 THR cc_start: 0.7626 (t) cc_final: 0.7336 (p)
REVERT: A  149 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8618 (mm-30)
REVERT: A  160 MET cc_start: 0.9386 (mmm) cc_final: 0.9053 (mmm)
REVERT: A  200 MET cc_start: 0.9431 (tmm) cc_final: 0.9132 (tmm)
REVERT: A  210 MET cc_start: 0.8802 (mmt) cc_final: 0.8165 (mmm)
REVERT: A  217 VAL cc_start: 0.9609 (t) cc_final: 0.9359 (t)
REVERT: A  226 GLU cc_start: 0.9183 (tp30) cc_final: 0.8957 (tp30)
REVERT: A  244 MET cc_start: 0.9400 (ppp) cc_final: 0.9061 (ppp)
REVERT: A  315 CYS cc_start: 0.8954 (t) cc_final: 0.8726 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 253
  average time/residue: 0.1700
  time to fit residues: 62.1460
Evaluate side-chains
  213 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 78 optimal weight:    5.9990
   chunk 35 optimal weight:    6.9990
   chunk 89 optimal weight:    7.9990
   chunk 57 optimal weight:    0.2980
   chunk 11 optimal weight:    0.4980
   chunk 70 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 40 optimal weight:    8.9990
   chunk 9 optimal weight:    1.9990
   chunk 60 optimal weight:    5.9990
   chunk 66 optimal weight:    7.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 527 GLN
A 537 HIS
A 574 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.076948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.056397 restraints weight = 33626.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.058717 restraints weight = 20755.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.060369 restraints weight = 14582.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.3569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8950  Z= 0.149
  Angle     :  0.600   6.894  12092  Z= 0.317
  Chirality :  0.041   0.208   1440
  Planarity :  0.004   0.046   1532
  Dihedral  :  4.571  19.647   1238
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.85 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.58 %
    Favored  : 97.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.85 (0.25), residues: 1134
  helix:  1.47 (0.19), residues: 728
  sheet:  0.19 (0.87), residues: 32
  loop : -1.22 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  66 
 HIS   0.003   0.001   HIS A 107 
 PHE   0.014   0.001   PHE A 115 
 TYR   0.014   0.001   TYR A 439 
 ARG   0.009   0.000   ARG B 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04384 (  557)
  hydrogen bonds       : angle       4.71107 ( 1656)
  covalent geometry    : bond        0.00304 ( 8950)
  covalent geometry    : angle       0.59975 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 245
  time to evaluate  : 1.064 
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: B   47 LEU cc_start: 0.9151 (mt) cc_final: 0.8940 (mt)
REVERT: B   98 MET cc_start: 0.9377 (ttt) cc_final: 0.8998 (ttt)
REVERT: B  100 MET cc_start: 0.9569 (ttp) cc_final: 0.9211 (tmm)
REVERT: B  111 MET cc_start: 0.9672 (ttt) cc_final: 0.9173 (ttp)
REVERT: B  115 PHE cc_start: 0.9118 (t80) cc_final: 0.8883 (t80)
REVERT: B  116 PHE cc_start: 0.8996 (m-10) cc_final: 0.8332 (m-80)
REVERT: B  149 GLU cc_start: 0.9080 (mp0) cc_final: 0.8753 (mp0)
REVERT: B  156 LEU cc_start: 0.9572 (mt) cc_final: 0.9334 (mt)
REVERT: B  160 MET cc_start: 0.9446 (mtm) cc_final: 0.9012 (mtm)
REVERT: B  200 MET cc_start: 0.9400 (tmm) cc_final: 0.9046 (tmm)
REVERT: B  208 GLU cc_start: 0.9137 (mp0) cc_final: 0.8844 (mp0)
REVERT: B  210 MET cc_start: 0.8739 (tpt) cc_final: 0.8531 (tpp)
REVERT: B  237 MET cc_start: 0.9172 (ttp) cc_final: 0.8518 (ptm)
REVERT: B  242 MET cc_start: 0.9114 (mmm) cc_final: 0.8858 (mmm)
REVERT: B  244 MET cc_start: 0.9307 (ppp) cc_final: 0.8979 (ppp)
REVERT: B  312 MET cc_start: 0.8685 (mmm) cc_final: 0.7772 (mmm)
REVERT: B  315 CYS cc_start: 0.8234 (m) cc_final: 0.7909 (m)
REVERT: B  538 ARG cc_start: 0.8420 (tpm170) cc_final: 0.8181 (tpp-160)
REVERT: A  109 MET cc_start: 0.8594 (mmp) cc_final: 0.8243 (tmm)
REVERT: A  111 MET cc_start: 0.9239 (tmm) cc_final: 0.9015 (tmm)
REVERT: A  149 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8806 (mm-30)
REVERT: A  160 MET cc_start: 0.9431 (mmm) cc_final: 0.9115 (mmm)
REVERT: A  200 MET cc_start: 0.9435 (tmm) cc_final: 0.9121 (tmm)
REVERT: A  210 MET cc_start: 0.8845 (mmt) cc_final: 0.8294 (mmm)
REVERT: A  217 VAL cc_start: 0.9645 (t) cc_final: 0.9288 (t)
REVERT: A  226 GLU cc_start: 0.9215 (tp30) cc_final: 0.8976 (tp30)
REVERT: A  244 MET cc_start: 0.9416 (ppp) cc_final: 0.9045 (ppp)
REVERT: A  312 MET cc_start: 0.8532 (mmm) cc_final: 0.7956 (mmm)
REVERT: A  390 THR cc_start: 0.9150 (p) cc_final: 0.8663 (p)
REVERT: A  392 PHE cc_start: 0.9315 (m-10) cc_final: 0.8997 (m-10)
REVERT: A  437 ILE cc_start: 0.9518 (tt) cc_final: 0.9290 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 245
  average time/residue: 0.1715
  time to fit residues: 60.9098
Evaluate side-chains
  205 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 4 optimal weight:    0.6980
   chunk 86 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9990
   chunk 55 optimal weight:   10.0000
   chunk 33 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 101 optimal weight:    2.9990
   chunk 106 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
A 214 HIS
A 537 HIS
A 574 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.077627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.056957 restraints weight = 33247.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.059295 restraints weight = 20667.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.061042 restraints weight = 14609.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.3801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8950  Z= 0.135
  Angle     :  0.578   6.007  12092  Z= 0.306
  Chirality :  0.041   0.201   1440
  Planarity :  0.004   0.046   1532
  Dihedral  :  4.568  19.504   1238
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.03 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.88 (0.25), residues: 1134
  helix:  1.51 (0.19), residues: 730
  sheet:  0.26 (0.88), residues: 32
  loop : -1.25 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  66 
 HIS   0.003   0.001   HIS B 214 
 PHE   0.013   0.001   PHE B 105 
 TYR   0.015   0.002   TYR A 439 
 ARG   0.008   0.000   ARG B 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04249 (  557)
  hydrogen bonds       : angle       4.58413 ( 1656)
  covalent geometry    : bond        0.00277 ( 8950)
  covalent geometry    : angle       0.57796 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 253
  time to evaluate  : 1.070 
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: B   98 MET cc_start: 0.9354 (ttt) cc_final: 0.8953 (ttt)
REVERT: B  100 MET cc_start: 0.9557 (ttp) cc_final: 0.9189 (tmm)
REVERT: B  108 MET cc_start: 0.9416 (mtm) cc_final: 0.9155 (ptp)
REVERT: B  111 MET cc_start: 0.9597 (ttt) cc_final: 0.9147 (ttp)
REVERT: B  115 PHE cc_start: 0.9080 (t80) cc_final: 0.8668 (t80)
REVERT: B  149 GLU cc_start: 0.9034 (mp0) cc_final: 0.8723 (mp0)
REVERT: B  156 LEU cc_start: 0.9558 (mt) cc_final: 0.9358 (mt)
REVERT: B  160 MET cc_start: 0.9427 (mtm) cc_final: 0.8983 (mtm)
REVERT: B  200 MET cc_start: 0.9388 (tmm) cc_final: 0.9041 (tmm)
REVERT: B  237 MET cc_start: 0.9129 (ttp) cc_final: 0.8901 (ppp)
REVERT: B  244 MET cc_start: 0.9327 (ppp) cc_final: 0.8975 (ppp)
REVERT: B  312 MET cc_start: 0.8763 (mmm) cc_final: 0.7948 (mmm)
REVERT: B  315 CYS cc_start: 0.8266 (m) cc_final: 0.7786 (m)
REVERT: B  456 MET cc_start: 0.9218 (mpp) cc_final: 0.8994 (mmp)
REVERT: B  538 ARG cc_start: 0.8418 (tpm170) cc_final: 0.8146 (tpp-160)
REVERT: A  109 MET cc_start: 0.8944 (mmp) cc_final: 0.8202 (tmm)
REVERT: A  115 PHE cc_start: 0.9022 (t80) cc_final: 0.8294 (t80)
REVERT: A  149 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8765 (mm-30)
REVERT: A  160 MET cc_start: 0.9424 (mmm) cc_final: 0.9103 (mmm)
REVERT: A  200 MET cc_start: 0.9434 (tmm) cc_final: 0.9113 (tmm)
REVERT: A  210 MET cc_start: 0.8842 (mmt) cc_final: 0.8310 (mmm)
REVERT: A  244 MET cc_start: 0.9379 (ppp) cc_final: 0.9008 (ppp)
REVERT: A  390 THR cc_start: 0.9125 (p) cc_final: 0.8627 (p)
REVERT: A  392 PHE cc_start: 0.9283 (m-10) cc_final: 0.8927 (m-10)
REVERT: A  437 ILE cc_start: 0.9488 (tt) cc_final: 0.9249 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 253
  average time/residue: 0.1720
  time to fit residues: 63.8197
Evaluate side-chains
  211 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 211
  time to evaluate  : 1.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 103 optimal weight:    0.9980
   chunk 100 optimal weight:    6.9990
   chunk 57 optimal weight:    0.7980
   chunk 104 optimal weight:    4.9990
   chunk 40 optimal weight:    9.9990
   chunk 70 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   chunk 71 optimal weight:    0.6980
   chunk 59 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 67 optimal weight:    3.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
** B 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 574 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.077770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.056941 restraints weight = 34066.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.059262 restraints weight = 21181.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.061026 restraints weight = 14974.542|
|-----------------------------------------------------------------------------|
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.3944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8950  Z= 0.139
  Angle     :  0.589   7.954  12092  Z= 0.311
  Chirality :  0.042   0.350   1440
  Planarity :  0.004   0.045   1532
  Dihedral  :  4.550  25.383   1238
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 13.41
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.03 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.92 (0.25), residues: 1134
  helix:  1.53 (0.19), residues: 730
  sheet:  0.31 (0.89), residues: 32
  loop : -1.23 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  66 
 HIS   0.004   0.001   HIS B 427 
 PHE   0.013   0.001   PHE B 105 
 TYR   0.012   0.001   TYR B 410 
 ARG   0.003   0.000   ARG A 229 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04213 (  557)
  hydrogen bonds       : angle       4.58155 ( 1656)
  covalent geometry    : bond        0.00287 ( 8950)
  covalent geometry    : angle       0.58921 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 247
  time to evaluate  : 1.102 
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: B   47 LEU cc_start: 0.9097 (mt) cc_final: 0.8886 (mt)
REVERT: B   98 MET cc_start: 0.9371 (ttt) cc_final: 0.9005 (ttt)
REVERT: B  100 MET cc_start: 0.9564 (ttp) cc_final: 0.9194 (tmm)
REVERT: B  108 MET cc_start: 0.9449 (mtm) cc_final: 0.9125 (ptp)
REVERT: B  111 MET cc_start: 0.9631 (ttt) cc_final: 0.9206 (ttt)
REVERT: B  115 PHE cc_start: 0.9060 (t80) cc_final: 0.8480 (t80)
REVERT: B  160 MET cc_start: 0.9437 (mtm) cc_final: 0.8991 (mtm)
REVERT: B  200 MET cc_start: 0.9404 (tmm) cc_final: 0.9050 (tmm)
REVERT: B  237 MET cc_start: 0.9150 (ttp) cc_final: 0.8468 (ptm)
REVERT: B  242 MET cc_start: 0.9007 (mmm) cc_final: 0.8776 (mmm)
REVERT: B  244 MET cc_start: 0.9331 (ppp) cc_final: 0.8969 (ppp)
REVERT: B  312 MET cc_start: 0.8783 (mmm) cc_final: 0.7936 (mmm)
REVERT: B  315 CYS cc_start: 0.8285 (m) cc_final: 0.7820 (m)
REVERT: A  109 MET cc_start: 0.8616 (mmp) cc_final: 0.8064 (tmm)
REVERT: A  111 MET cc_start: 0.9172 (tmm) cc_final: 0.8870 (tmm)
REVERT: A  115 PHE cc_start: 0.9132 (t80) cc_final: 0.8528 (t80)
REVERT: A  121 THR cc_start: 0.7734 (t) cc_final: 0.7450 (p)
REVERT: A  149 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8762 (mm-30)
REVERT: A  156 LEU cc_start: 0.9669 (mt) cc_final: 0.9434 (mt)
REVERT: A  160 MET cc_start: 0.9407 (mmm) cc_final: 0.9101 (mmm)
REVERT: A  174 LEU cc_start: 0.9267 (mt) cc_final: 0.9043 (mt)
REVERT: A  200 MET cc_start: 0.9449 (tmm) cc_final: 0.9138 (tmm)
REVERT: A  210 MET cc_start: 0.8800 (mmt) cc_final: 0.8280 (mmm)
REVERT: A  244 MET cc_start: 0.9379 (ppp) cc_final: 0.8990 (ppp)
REVERT: A  312 MET cc_start: 0.8382 (mmm) cc_final: 0.7693 (mmt)
REVERT: A  315 CYS cc_start: 0.8982 (t) cc_final: 0.8748 (t)
REVERT: A  390 THR cc_start: 0.9124 (p) cc_final: 0.8666 (p)
REVERT: A  392 PHE cc_start: 0.9295 (m-10) cc_final: 0.8939 (m-10)
REVERT: A  437 ILE cc_start: 0.9496 (tt) cc_final: 0.9251 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 247
  average time/residue: 0.1759
  time to fit residues: 63.2691
Evaluate side-chains
  207 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 40 optimal weight:    9.9990
   chunk 96 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 102 optimal weight:    5.9990
   chunk 99 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.9986

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
** A 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 574 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.077725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.057097 restraints weight = 33867.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.059398 restraints weight = 21110.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.061122 restraints weight = 14932.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.4126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8950  Z= 0.134
  Angle     :  0.593   8.154  12092  Z= 0.311
  Chirality :  0.043   0.309   1440
  Planarity :  0.003   0.045   1532
  Dihedral  :  4.511  23.704   1238
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.03 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.00 (0.25), residues: 1134
  helix:  1.58 (0.19), residues: 730
  sheet:  0.39 (0.89), residues: 32
  loop : -1.18 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A  66 
 HIS   0.003   0.001   HIS B 214 
 PHE   0.013   0.001   PHE B 344 
 TYR   0.016   0.001   TYR A 439 
 ARG   0.003   0.000   ARG A 229 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04183 (  557)
  hydrogen bonds       : angle       4.53439 ( 1656)
  covalent geometry    : bond        0.00281 ( 8950)
  covalent geometry    : angle       0.59336 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 245
  time to evaluate  : 0.881 
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: B   47 LEU cc_start: 0.9111 (mt) cc_final: 0.8900 (mt)
REVERT: B   98 MET cc_start: 0.9351 (ttt) cc_final: 0.8978 (ttt)
REVERT: B  100 MET cc_start: 0.9560 (ttp) cc_final: 0.9206 (tmm)
REVERT: B  108 MET cc_start: 0.9450 (mtm) cc_final: 0.9073 (mtp)
REVERT: B  111 MET cc_start: 0.9622 (ttt) cc_final: 0.9326 (ttt)
REVERT: B  160 MET cc_start: 0.9451 (mtm) cc_final: 0.9010 (mtm)
REVERT: B  200 MET cc_start: 0.9403 (tmm) cc_final: 0.9053 (tmm)
REVERT: B  210 MET cc_start: 0.8714 (tpt) cc_final: 0.8197 (mmm)
REVERT: B  226 GLU cc_start: 0.9567 (tm-30) cc_final: 0.9275 (tm-30)
REVERT: B  237 MET cc_start: 0.9154 (ttp) cc_final: 0.8510 (ptm)
REVERT: B  242 MET cc_start: 0.9028 (mmm) cc_final: 0.8806 (mmm)
REVERT: B  244 MET cc_start: 0.9331 (ppp) cc_final: 0.8958 (ppp)
REVERT: B  312 MET cc_start: 0.8841 (mmm) cc_final: 0.8450 (mmm)
REVERT: B  315 CYS cc_start: 0.8305 (m) cc_final: 0.8021 (m)
REVERT: B  402 MET cc_start: 0.8793 (tmm) cc_final: 0.8554 (tmm)
REVERT: B  456 MET cc_start: 0.9195 (mpp) cc_final: 0.8970 (mmp)
REVERT: B  538 ARG cc_start: 0.8463 (tpm170) cc_final: 0.8109 (tpm170)
REVERT: A   67 MET cc_start: 0.8460 (mmp) cc_final: 0.8245 (mmp)
REVERT: A  111 MET cc_start: 0.9150 (tmm) cc_final: 0.8871 (tmm)
REVERT: A  115 PHE cc_start: 0.9181 (t80) cc_final: 0.8683 (t80)
REVERT: A  149 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8810 (mm-30)
REVERT: A  156 LEU cc_start: 0.9646 (mt) cc_final: 0.9435 (mt)
REVERT: A  160 MET cc_start: 0.9415 (mmm) cc_final: 0.9112 (mmm)
REVERT: A  196 MET cc_start: 0.8928 (mmp) cc_final: 0.8289 (mmt)
REVERT: A  200 MET cc_start: 0.9448 (tmm) cc_final: 0.9145 (tmm)
REVERT: A  210 MET cc_start: 0.8811 (mmt) cc_final: 0.8318 (mmm)
REVERT: A  217 VAL cc_start: 0.9557 (t) cc_final: 0.9275 (t)
REVERT: A  244 MET cc_start: 0.9375 (ppp) cc_final: 0.8972 (ppp)
REVERT: A  315 CYS cc_start: 0.8986 (t) cc_final: 0.8756 (t)
REVERT: A  392 PHE cc_start: 0.9301 (m-10) cc_final: 0.8942 (m-10)
REVERT: A  410 TYR cc_start: 0.8275 (m-10) cc_final: 0.7847 (m-80)
REVERT: A  437 ILE cc_start: 0.9489 (tt) cc_final: 0.9248 (tp)
REVERT: A  456 MET cc_start: 0.9186 (mmp) cc_final: 0.8985 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 245
  average time/residue: 0.2022
  time to fit residues: 73.0998
Evaluate side-chains
  209 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 209
  time to evaluate  : 1.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 74 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0370
   chunk 78 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 79 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 87 optimal weight:    0.6980
   chunk 77 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 32 optimal weight:    6.9990
   overall best weight:    0.6858

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

Flipped N/Q/H residues before XYZ refinement:
** A 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 574 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.078647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.057974 restraints weight = 33036.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.060322 restraints weight = 20677.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.061925 restraints weight = 14625.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.4258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8950  Z= 0.128
  Angle     :  0.608   8.067  12092  Z= 0.316
  Chirality :  0.043   0.294   1440
  Planarity :  0.003   0.045   1532
  Dihedral  :  4.457  22.868   1238
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 12.63
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.94 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.01 (0.25), residues: 1134
  helix:  1.59 (0.19), residues: 730
  sheet:  0.54 (0.90), residues: 32
  loop : -1.18 (0.34), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  66 
 HIS   0.004   0.001   HIS A 107 
 PHE   0.013   0.001   PHE B 344 
 TYR   0.013   0.001   TYR A 439 
 ARG   0.003   0.000   ARG A 229 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04075 (  557)
  hydrogen bonds       : angle       4.54009 ( 1656)
  covalent geometry    : bond        0.00269 ( 8950)
  covalent geometry    : angle       0.60835 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 246
  time to evaluate  : 1.068 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   47 LEU cc_start: 0.9109 (mt) cc_final: 0.8894 (mt)
REVERT: B   98 MET cc_start: 0.9347 (ttt) cc_final: 0.8981 (ttt)
REVERT: B  100 MET cc_start: 0.9560 (ttp) cc_final: 0.9198 (tmm)
REVERT: B  111 MET cc_start: 0.9575 (ttt) cc_final: 0.9110 (ttp)
REVERT: B  115 PHE cc_start: 0.8944 (t80) cc_final: 0.8532 (t80)
REVERT: B  116 PHE cc_start: 0.8760 (m-10) cc_final: 0.7529 (m-10)
REVERT: B  160 MET cc_start: 0.9461 (mtm) cc_final: 0.9010 (mtm)
REVERT: B  200 MET cc_start: 0.9406 (tmm) cc_final: 0.9063 (tmm)
REVERT: B  208 GLU cc_start: 0.9165 (mp0) cc_final: 0.8934 (mp0)
REVERT: B  210 MET cc_start: 0.8635 (tpt) cc_final: 0.8042 (tpp)
REVERT: B  226 GLU cc_start: 0.9549 (tm-30) cc_final: 0.9170 (tp30)
REVERT: B  242 MET cc_start: 0.9011 (mmm) cc_final: 0.8785 (mmm)
REVERT: B  244 MET cc_start: 0.9337 (ppp) cc_final: 0.8959 (ppp)
REVERT: B  295 MET cc_start: 0.8097 (ttt) cc_final: 0.7833 (ttp)
REVERT: B  312 MET cc_start: 0.8832 (mmm) cc_final: 0.8451 (mmm)
REVERT: B  315 CYS cc_start: 0.8318 (m) cc_final: 0.8040 (m)
REVERT: B  402 MET cc_start: 0.8798 (tmm) cc_final: 0.8544 (tmm)
REVERT: B  456 MET cc_start: 0.9203 (mpp) cc_final: 0.8985 (mmp)
REVERT: B  527 GLN cc_start: 0.9323 (pt0) cc_final: 0.9085 (pp30)
REVERT: B  538 ARG cc_start: 0.8455 (tpm170) cc_final: 0.8096 (tpp-160)
REVERT: A  109 MET cc_start: 0.8564 (mmp) cc_final: 0.7690 (tmm)
REVERT: A  111 MET cc_start: 0.9123 (tmm) cc_final: 0.8650 (tmm)
REVERT: A  115 PHE cc_start: 0.9133 (t80) cc_final: 0.8624 (t80)
REVERT: A  116 PHE cc_start: 0.8963 (m-80) cc_final: 0.8198 (m-80)
REVERT: A  156 LEU cc_start: 0.9648 (mt) cc_final: 0.9443 (mt)
REVERT: A  160 MET cc_start: 0.9412 (mmm) cc_final: 0.9107 (mmm)
REVERT: A  180 ILE cc_start: 0.8998 (tt) cc_final: 0.8796 (pt)
REVERT: A  196 MET cc_start: 0.8914 (mmp) cc_final: 0.8238 (mmp)
REVERT: A  200 MET cc_start: 0.9443 (tmm) cc_final: 0.9140 (tmm)
REVERT: A  210 MET cc_start: 0.8830 (mmt) cc_final: 0.8317 (mmm)
REVERT: A  217 VAL cc_start: 0.9500 (t) cc_final: 0.9241 (t)
REVERT: A  244 MET cc_start: 0.9375 (ppp) cc_final: 0.8984 (ppp)
REVERT: A  312 MET cc_start: 0.8222 (mmm) cc_final: 0.7864 (mmm)
REVERT: A  315 CYS cc_start: 0.8978 (t) cc_final: 0.8750 (t)
REVERT: A  390 THR cc_start: 0.9141 (p) cc_final: 0.8783 (p)
REVERT: A  392 PHE cc_start: 0.9303 (m-10) cc_final: 0.8938 (m-10)
REVERT: A  410 TYR cc_start: 0.8264 (m-10) cc_final: 0.7798 (m-80)
REVERT: A  437 ILE cc_start: 0.9480 (tt) cc_final: 0.9214 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 246
  average time/residue: 0.1980
  time to fit residues: 71.7704
Evaluate side-chains
  210 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 1.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 95 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 87 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   chunk 73 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 88 optimal weight:   10.0000
   chunk 100 optimal weight:    6.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** A 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 574 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.077629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.056860 restraints weight = 33680.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.059146 restraints weight = 21301.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.060840 restraints weight = 15153.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.4404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8950  Z= 0.139
  Angle     :  0.617   7.182  12092  Z= 0.323
  Chirality :  0.043   0.280   1440
  Planarity :  0.004   0.047   1532
  Dihedral  :  4.476  22.985   1238
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 13.52
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.76 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.99 (0.25), residues: 1134
  helix:  1.56 (0.19), residues: 734
  sheet: -0.41 (0.75), residues: 46
  loop : -1.10 (0.35), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A  66 
 HIS   0.004   0.001   HIS A 214 
 PHE   0.012   0.001   PHE B 344 
 TYR   0.015   0.001   TYR A 439 
 ARG   0.009   0.000   ARG B 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04139 (  557)
  hydrogen bonds       : angle       4.57782 ( 1656)
  covalent geometry    : bond        0.00292 ( 8950)
  covalent geometry    : angle       0.61700 (12092)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 1.333 
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: B   47 LEU cc_start: 0.9141 (mt) cc_final: 0.8917 (mt)
REVERT: B   98 MET cc_start: 0.9357 (ttt) cc_final: 0.8972 (ttt)
REVERT: B  100 MET cc_start: 0.9553 (ttp) cc_final: 0.9187 (tmm)
REVERT: B  111 MET cc_start: 0.9611 (ttt) cc_final: 0.9146 (ttp)
REVERT: B  115 PHE cc_start: 0.8916 (t80) cc_final: 0.8485 (t80)
REVERT: B  116 PHE cc_start: 0.8797 (m-10) cc_final: 0.7351 (m-10)
REVERT: B  156 LEU cc_start: 0.9522 (mt) cc_final: 0.9306 (mt)
REVERT: B  160 MET cc_start: 0.9453 (mtm) cc_final: 0.9001 (mtm)
REVERT: B  200 MET cc_start: 0.9431 (tmm) cc_final: 0.9048 (tmm)
REVERT: B  203 VAL cc_start: 0.9385 (t) cc_final: 0.9160 (p)
REVERT: B  208 GLU cc_start: 0.9137 (mp0) cc_final: 0.8901 (mp0)
REVERT: B  210 MET cc_start: 0.8637 (tpt) cc_final: 0.8081 (mmm)
REVERT: B  244 MET cc_start: 0.9350 (ppp) cc_final: 0.8972 (ppp)
REVERT: B  295 MET cc_start: 0.8141 (ttt) cc_final: 0.7878 (ttp)
REVERT: B  312 MET cc_start: 0.8895 (mmm) cc_final: 0.7974 (mmm)
REVERT: B  315 CYS cc_start: 0.8329 (m) cc_final: 0.8030 (m)
REVERT: B  456 MET cc_start: 0.9221 (mpp) cc_final: 0.9005 (mmp)
REVERT: B  503 ILE cc_start: 0.9742 (mm) cc_final: 0.9498 (tp)
REVERT: B  527 GLN cc_start: 0.9324 (pt0) cc_final: 0.9087 (pp30)
REVERT: B  538 ARG cc_start: 0.8496 (tpm170) cc_final: 0.8101 (tpm170)
REVERT: A   67 MET cc_start: 0.8389 (mmp) cc_final: 0.8117 (mmp)
REVERT: A  109 MET cc_start: 0.8634 (mmp) cc_final: 0.7533 (tmm)
REVERT: A  111 MET cc_start: 0.9104 (tmm) cc_final: 0.8657 (tmm)
REVERT: A  115 PHE cc_start: 0.9143 (t80) cc_final: 0.8641 (t80)
REVERT: A  116 PHE cc_start: 0.8948 (m-80) cc_final: 0.8241 (m-80)
REVERT: A  156 LEU cc_start: 0.9674 (mt) cc_final: 0.9412 (mt)
REVERT: A  160 MET cc_start: 0.9399 (mmm) cc_final: 0.9060 (mmm)
REVERT: A  180 ILE cc_start: 0.8998 (tt) cc_final: 0.8795 (pt)
REVERT: A  196 MET cc_start: 0.8910 (mmp) cc_final: 0.8242 (mmp)
REVERT: A  200 MET cc_start: 0.9438 (tmm) cc_final: 0.9130 (tmm)
REVERT: A  210 MET cc_start: 0.8687 (mmt) cc_final: 0.8332 (mmm)
REVERT: A  217 VAL cc_start: 0.9446 (t) cc_final: 0.9227 (t)
REVERT: A  244 MET cc_start: 0.9378 (ppp) cc_final: 0.8987 (ppp)
REVERT: A  312 MET cc_start: 0.8316 (mmm) cc_final: 0.7573 (mmm)
REVERT: A  315 CYS cc_start: 0.8996 (t) cc_final: 0.8762 (t)
REVERT: A  390 THR cc_start: 0.9096 (p) cc_final: 0.8763 (p)
REVERT: A  392 PHE cc_start: 0.9282 (m-10) cc_final: 0.8929 (m-10)
REVERT: A  410 TYR cc_start: 0.8284 (m-10) cc_final: 0.7849 (m-80)
REVERT: A  437 ILE cc_start: 0.9481 (tt) cc_final: 0.9232 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 242
  average time/residue: 0.2129
  time to fit residues: 77.9683
Evaluate side-chains
  206 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 0.980 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 78 optimal weight:    0.8980
   chunk 37 optimal weight:    8.9990
   chunk 12 optimal weight:    2.9990
   chunk 40 optimal weight:   10.0000
   chunk 53 optimal weight:    0.8980
   chunk 86 optimal weight:    4.9990
   chunk 54 optimal weight:    9.9990
   chunk 111 optimal weight:    4.9990
   chunk 102 optimal weight:   20.0000
   chunk 84 optimal weight:    0.3980
   chunk 87 optimal weight:    2.9990
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 574 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.076679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.055612 restraints weight = 34141.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.057861 restraints weight = 21651.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.059511 restraints weight = 15443.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.4419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8950  Z= 0.164
  Angle     :  0.640   8.664  12092  Z= 0.334
  Chirality :  0.043   0.270   1440
  Planarity :  0.004   0.045   1532
  Dihedral  :  4.515  22.965   1238
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 14.41
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.94 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.05 (0.25), residues: 1134
  helix:  1.60 (0.19), residues: 734
  sheet: -0.38 (0.73), residues: 48
  loop : -1.06 (0.35), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A  17 
 HIS   0.008   0.001   HIS A 214 
 PHE   0.013   0.001   PHE B 344 
 TYR   0.014   0.002   TYR B 410 
 ARG   0.007   0.000   ARG A  14 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04245 (  557)
  hydrogen bonds       : angle       4.65974 ( 1656)
  covalent geometry    : bond        0.00338 ( 8950)
  covalent geometry    : angle       0.64017 (12092)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3940.99 seconds
wall clock time: 69 minutes 22.90 seconds (4162.90 seconds total)