Starting phenix.real_space_refine
on Mon May 12 09:12:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fuz_50783/05_2025/9fuz_50783.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fuz_50783/05_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_50783/05_2025/9fuz_50783.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fuz_50783/05_2025/9fuz_50783.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fuz_50783/05_2025/9fuz_50783.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fuz_50783/05_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-5687/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: 5.75, per 1000 atoms: 0.65
  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: 2.25
  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: 2.42

  Time building geometry restraints manager: 2.62 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:             3.230
  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:          0.480
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     22.390
  Find NCS groups from input model:        0.270
  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:             0.010
  Load rotamer database and sin/cos tables:2.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.200
-------------------------------------------------------------------------------
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  : 1.005 
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: 0.1698
  time to fit residues: 55.5106
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  : 0.955 
-------------------------------------------------------------------------------
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:    3.9990
   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:    1.7990

-------------------------------------------------------------------------------
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 = 0.3425 r_free = 0.3425 target = 0.076066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.055787 restraints weight = 33761.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.057999 restraints weight = 20768.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.059663 restraints weight = 14634.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.2400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   8950  Z= 0.186
  Angle     :  0.637   8.074  12092  Z= 0.347
  Chirality :  0.043   0.212   1440
  Planarity :  0.005   0.062   1532
  Dihedral  :  4.943  20.140   1238
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.20 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  4.24 %
    Favored  : 95.66 %
  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:  0.46 (0.25), residues: 1134
  helix:  1.14 (0.18), residues: 730
  sheet: -0.17 (0.85), residues: 36
  loop : -1.30 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 165 
 HIS   0.004   0.001   HIS B 214 
 PHE   0.024   0.002   PHE B 157 
 TYR   0.016   0.002   TYR A 572 
 ARG   0.007   0.001   ARG A 360 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05356 (  557)
  hydrogen bonds       : angle       5.16470 ( 1656)
  covalent geometry    : bond        0.00373 ( 8950)
  covalent geometry    : angle       0.63727 (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
  246 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 245
  time to evaluate  : 1.107 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   98 MET cc_start: 0.9370 (ttt) cc_final: 0.9042 (ttt)
REVERT: B  100 MET cc_start: 0.9608 (ttp) cc_final: 0.9339 (tmm)
REVERT: B  115 PHE cc_start: 0.9428 (t80) cc_final: 0.8836 (t80)
REVERT: B  200 MET cc_start: 0.9312 (tmm) cc_final: 0.8961 (tmm)
REVERT: B  226 GLU cc_start: 0.9390 (tp30) cc_final: 0.9138 (tp30)
REVERT: B  242 MET cc_start: 0.9112 (mmm) cc_final: 0.8847 (mmm)
REVERT: B  244 MET cc_start: 0.9276 (ppp) cc_final: 0.8963 (ppp)
REVERT: B  332 LYS cc_start: 0.9665 (mttt) cc_final: 0.9383 (mmtt)
REVERT: B  359 LEU cc_start: 0.9612 (tp) cc_final: 0.9345 (tp)
REVERT: B  360 ARG cc_start: 0.9587 (ttt180) cc_final: 0.9376 (mmm160)
REVERT: B  527 GLN cc_start: 0.9342 (pt0) cc_final: 0.9113 (pp30)
REVERT: A   98 MET cc_start: 0.9263 (ttm) cc_final: 0.8909 (ttt)
REVERT: A  109 MET cc_start: 0.8693 (mmp) cc_final: 0.8342 (tmm)
REVERT: A  149 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8654 (mm-30)
REVERT: A  160 MET cc_start: 0.9351 (mmm) cc_final: 0.9025 (mmm)
REVERT: A  200 MET cc_start: 0.9448 (tmm) cc_final: 0.9197 (tmm)
REVERT: A  210 MET cc_start: 0.8812 (mmt) cc_final: 0.8453 (mmm)
REVERT: A  244 MET cc_start: 0.9374 (ppp) cc_final: 0.9096 (ppp)
REVERT: A  390 THR cc_start: 0.9168 (p) cc_final: 0.8612 (p)
REVERT: A  392 PHE cc_start: 0.9335 (m-10) cc_final: 0.9097 (m-10)
REVERT: A  456 MET cc_start: 0.9163 (mmp) cc_final: 0.8946 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 245
  average time/residue: 0.1696
  time to fit residues: 60.8916
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=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 79 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 48 optimal weight:    7.9990
   chunk 82 optimal weight:   10.0000
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 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 = 0.3432 r_free = 0.3432 target = 0.076096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.055801 restraints weight = 34080.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.058073 restraints weight = 21154.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.059768 restraints weight = 14891.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.3008

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= 0.156
  Angle     :  0.612   6.965  12092  Z= 0.327
  Chirality :  0.042   0.176   1440
  Planarity :  0.006   0.147   1532
  Dihedral  :  4.829  18.898   1238
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.76 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  4.03 %
    Favored  : 95.76 %
  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:  0.74 (0.25), residues: 1134
  helix:  1.35 (0.19), residues: 726
  sheet:  0.16 (0.86), residues: 32
  loop : -1.18 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A  66 
 HIS   0.006   0.001   HIS B 576 
 PHE   0.014   0.002   PHE B 157 
 TYR   0.016   0.002   TYR B 410 
 ARG   0.014   0.001   ARG A 530 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04789 (  557)
  hydrogen bonds       : angle       4.94018 ( 1656)
  covalent geometry    : bond        0.00318 ( 8950)
  covalent geometry    : angle       0.61231 (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
  249 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 247
  time to evaluate  : 1.006 
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: 0.9384 (ttt) cc_final: 0.9033 (ttt)
REVERT: B  100 MET cc_start: 0.9575 (ttp) cc_final: 0.9309 (tmm)
REVERT: B  115 PHE cc_start: 0.9065 (t80) cc_final: 0.8674 (t80)
REVERT: B  116 PHE cc_start: 0.9122 (m-10) cc_final: 0.8905 (m-10)
REVERT: B  200 MET cc_start: 0.9378 (tmm) cc_final: 0.9034 (tmm)
REVERT: B  210 MET cc_start: 0.8666 (tpt) cc_final: 0.8450 (tpp)
REVERT: B  242 MET cc_start: 0.9131 (mmm) cc_final: 0.8897 (mmm)
REVERT: B  244 MET cc_start: 0.9286 (ppp) cc_final: 0.8928 (ppp)
REVERT: B  312 MET cc_start: 0.8573 (ttt) cc_final: 0.8167 (mmm)
REVERT: B  315 CYS cc_start: 0.8016 (m) cc_final: 0.7705 (m)
REVERT: B  359 LEU cc_start: 0.9592 (tp) cc_final: 0.9342 (tp)
REVERT: B  360 ARG cc_start: 0.9605 (ttt180) cc_final: 0.9384 (mmm160)
REVERT: B  527 GLN cc_start: 0.9377 (pt0) cc_final: 0.9130 (pp30)
REVERT: B  538 ARG cc_start: 0.8370 (tpm170) cc_final: 0.8138 (tpp-160)
REVERT: A   98 MET cc_start: 0.9220 (ttm) cc_final: 0.9019 (ttt)
REVERT: A  109 MET cc_start: 0.8919 (mmp) cc_final: 0.8294 (tmm)
REVERT: A  115 PHE cc_start: 0.9031 (t80) cc_final: 0.8372 (t80)
REVERT: A  116 PHE cc_start: 0.8954 (m-80) cc_final: 0.8563 (m-80)
REVERT: A  160 MET cc_start: 0.9341 (mmm) cc_final: 0.8999 (mmm)
REVERT: A  200 MET cc_start: 0.9432 (tmm) cc_final: 0.9151 (tmm)
REVERT: A  210 MET cc_start: 0.8800 (mmt) cc_final: 0.8261 (mmm)
REVERT: A  226 GLU cc_start: 0.9312 (tp30) cc_final: 0.9030 (tp30)
REVERT: A  315 CYS cc_start: 0.8888 (t) cc_final: 0.8678 (t)
REVERT: A  392 PHE cc_start: 0.9305 (m-10) cc_final: 0.8949 (m-10)
  outliers start: 2
  outliers final: 0
  residues processed: 248
  average time/residue: 0.1839
  time to fit residues: 64.5383
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  : 1.055 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 5 optimal weight:    0.0980
   chunk 23 optimal weight:    7.9990
   chunk 98 optimal weight:    4.9990
   chunk 39 optimal weight:    9.9990
   chunk 16 optimal weight:    0.9980
   chunk 92 optimal weight:   10.0000
   chunk 99 optimal weight:    3.9990
   chunk 107 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 77 optimal weight:    0.0970
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 = 0.3469 r_free = 0.3469 target = 0.078059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.057230 restraints weight = 33208.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.059552 restraints weight = 20553.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.061322 restraints weight = 14539.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.3363

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     :  0.576   6.307  12092  Z= 0.306
  Chirality :  0.042   0.215   1440
  Planarity :  0.004   0.050   1532
  Dihedral  :  4.631  19.061   1238
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.11 %
    Favored  : 94.62 %
  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:  0.85 (0.25), residues: 1134
  helix:  1.40 (0.19), residues: 730
  sheet:  0.33 (0.88), residues: 32
  loop : -1.08 (0.34), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  66 
 HIS   0.003   0.001   HIS B 214 
 PHE   0.013   0.001   PHE B 288 
 TYR   0.015   0.001   TYR B 410 
 ARG   0.007   0.000   ARG B 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04392 (  557)
  hydrogen bonds       : angle       4.69305 ( 1656)
  covalent geometry    : bond        0.00266 ( 8950)
  covalent geometry    : angle       0.57567 (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
  251 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 250
  time to evaluate  : 0.964 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   98 MET cc_start: 0.9359 (ttt) cc_final: 0.9008 (ttt)
REVERT: B  100 MET cc_start: 0.9542 (ttp) cc_final: 0.9294 (tmm)
REVERT: B  108 MET cc_start: 0.9339 (mtm) cc_final: 0.9093 (ptp)
REVERT: B  111 MET cc_start: 0.9068 (ttp) cc_final: 0.8832 (ttp)
REVERT: B  115 PHE cc_start: 0.9163 (t80) cc_final: 0.8852 (t80)
REVERT: B  149 GLU cc_start: 0.8993 (mp0) cc_final: 0.8645 (mp0)
REVERT: B  200 MET cc_start: 0.9380 (tmm) cc_final: 0.9019 (tmm)
REVERT: B  208 GLU cc_start: 0.9083 (mp0) cc_final: 0.8799 (mt-10)
REVERT: B  210 MET cc_start: 0.8685 (tpt) cc_final: 0.8453 (tpp)
REVERT: B  242 MET cc_start: 0.9074 (mmm) cc_final: 0.8818 (mmm)
REVERT: B  244 MET cc_start: 0.9284 (ppp) cc_final: 0.8909 (ppp)
REVERT: B  312 MET cc_start: 0.8436 (ttt) cc_final: 0.7920 (mmm)
REVERT: B  315 CYS cc_start: 0.8119 (m) cc_final: 0.7837 (m)
REVERT: B  527 GLN cc_start: 0.9357 (pt0) cc_final: 0.9113 (pp30)
REVERT: B  538 ARG cc_start: 0.8385 (tpm170) cc_final: 0.8135 (tpp-160)
REVERT: A  109 MET cc_start: 0.8876 (mmp) cc_final: 0.8247 (tmm)
REVERT: A  111 MET cc_start: 0.9095 (tmm) cc_final: 0.8707 (tmm)
REVERT: A  115 PHE cc_start: 0.8997 (t80) cc_final: 0.8794 (t80)
REVERT: A  116 PHE cc_start: 0.8939 (m-80) cc_final: 0.8443 (m-80)
REVERT: A  121 THR cc_start: 0.7607 (t) cc_final: 0.7321 (p)
REVERT: A  149 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8707 (mm-30)
REVERT: A  160 MET cc_start: 0.9376 (mmm) cc_final: 0.9084 (mmm)
REVERT: A  200 MET cc_start: 0.9427 (tmm) cc_final: 0.9130 (tmm)
REVERT: A  210 MET cc_start: 0.8769 (mmt) cc_final: 0.8148 (mmm)
REVERT: A  217 VAL cc_start: 0.9515 (t) cc_final: 0.9282 (t)
REVERT: A  244 MET cc_start: 0.9371 (ppp) cc_final: 0.9079 (ppp)
REVERT: A  291 MET cc_start: 0.9582 (tpp) cc_final: 0.9354 (tpt)
REVERT: A  295 MET cc_start: 0.8644 (ttt) cc_final: 0.8294 (ttp)
REVERT: A  315 CYS cc_start: 0.8968 (t) cc_final: 0.8762 (t)
REVERT: A  390 THR cc_start: 0.9099 (p) cc_final: 0.8709 (p)
REVERT: A  392 PHE cc_start: 0.9258 (m-10) cc_final: 0.8886 (m-10)
  outliers start: 1
  outliers final: 0
  residues processed: 250
  average time/residue: 0.1658
  time to fit residues: 59.8115
Evaluate side-chains
  216 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 89 optimal weight:    5.9990
   chunk 57 optimal weight:    0.7980
   chunk 11 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9980
   chunk 65 optimal weight:    4.9990
   chunk 40 optimal weight:   10.0000
   chunk 9 optimal weight:    0.9990
   chunk 60 optimal weight:   10.0000
   chunk 66 optimal weight:    3.9990
   overall best weight:    2.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 527 GLN ** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.074504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.053953 restraints weight = 34409.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.056174 restraints weight = 21221.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.057815 restraints weight = 14924.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.3591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   8950  Z= 0.206
  Angle     :  0.636   7.950  12092  Z= 0.342
  Chirality :  0.042   0.183   1440
  Planarity :  0.004   0.047   1532
  Dihedral  :  4.653  20.272   1238
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 14.25
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.29 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.48 %
    Favored  : 97.42 %
  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:  0.76 (0.25), residues: 1134
  helix:  1.41 (0.19), residues: 732
  sheet: -0.85 (0.72), residues: 44
  loop : -1.18 (0.34), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A  66 
 HIS   0.005   0.001   HIS B 214 
 PHE   0.017   0.002   PHE B 105 
 TYR   0.013   0.002   TYR B 410 
 ARG   0.008   0.000   ARG B 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04724 (  557)
  hydrogen bonds       : angle       4.85275 ( 1656)
  covalent geometry    : bond        0.00400 ( 8950)
  covalent geometry    : angle       0.63621 (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
  241 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 240
  time to evaluate  : 0.990 
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: 0.9158 (mt) cc_final: 0.8954 (mt)
REVERT: B   98 MET cc_start: 0.9370 (ttt) cc_final: 0.8998 (ttt)
REVERT: B  100 MET cc_start: 0.9569 (ttp) cc_final: 0.9208 (tmm)
REVERT: B  108 MET cc_start: 0.9519 (mtm) cc_final: 0.9164 (mtp)
REVERT: B  149 GLU cc_start: 0.9100 (mp0) cc_final: 0.8760 (mp0)
REVERT: B  200 MET cc_start: 0.9423 (tmm) cc_final: 0.9081 (tmm)
REVERT: B  210 MET cc_start: 0.8877 (tpt) cc_final: 0.8519 (tpp)
REVERT: B  229 ARG cc_start: 0.9199 (ttm-80) cc_final: 0.8846 (ttm-80)
REVERT: B  244 MET cc_start: 0.9307 (ppp) cc_final: 0.8922 (ppp)
REVERT: A   67 MET cc_start: 0.8459 (mmp) cc_final: 0.8242 (mmp)
REVERT: A  109 MET cc_start: 0.8670 (mmp) cc_final: 0.8356 (tmm)
REVERT: A  115 PHE cc_start: 0.9060 (t80) cc_final: 0.8791 (t80)
REVERT: A  160 MET cc_start: 0.9361 (mmm) cc_final: 0.9041 (mmm)
REVERT: A  200 MET cc_start: 0.9456 (tmm) cc_final: 0.9154 (tmm)
REVERT: A  210 MET cc_start: 0.8837 (mmt) cc_final: 0.8374 (mmm)
REVERT: A  226 GLU cc_start: 0.9249 (tp30) cc_final: 0.9009 (tp30)
REVERT: A  244 MET cc_start: 0.9375 (ppp) cc_final: 0.9058 (ppp)
REVERT: A  312 MET cc_start: 0.8643 (mmm) cc_final: 0.8109 (mmm)
REVERT: A  315 CYS cc_start: 0.8998 (t) cc_final: 0.8792 (t)
REVERT: A  390 THR cc_start: 0.9014 (p) cc_final: 0.8638 (p)
REVERT: A  392 PHE cc_start: 0.9341 (m-10) cc_final: 0.8985 (m-10)
REVERT: A  437 ILE cc_start: 0.9517 (tt) cc_final: 0.9292 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 240
  average time/residue: 0.1684
  time to fit residues: 58.6808
Evaluate side-chains
  203 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 86 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 55 optimal weight:    6.9990
   chunk 33 optimal weight:    7.9990
   chunk 21 optimal weight:    4.9990
   chunk 101 optimal weight:    0.5980
   chunk 106 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 527 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 = 0.3438 r_free = 0.3438 target = 0.076808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.055947 restraints weight = 33479.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.058265 restraints weight = 20705.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.059975 restraints weight = 14545.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.3786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   8950  Z= 0.137
  Angle     :  0.599   6.869  12092  Z= 0.316
  Chirality :  0.043   0.335   1440
  Planarity :  0.004   0.048   1532
  Dihedral  :  4.626  19.610   1238
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 12.63
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.11 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  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:  0.80 (0.25), residues: 1134
  helix:  1.44 (0.19), residues: 728
  sheet:  0.19 (0.89), residues: 32
  loop : -1.27 (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 B 214 
 PHE   0.011   0.001   PHE B 105 
 TYR   0.016   0.001   TYR B 351 
 ARG   0.006   0.000   ARG B 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04317 (  557)
  hydrogen bonds       : angle       4.69734 ( 1656)
  covalent geometry    : bond        0.00287 ( 8950)
  covalent geometry    : angle       0.59945 (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
  240 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 240
  time to evaluate  : 1.001 
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: 0.9120 (mt) cc_final: 0.8905 (mt)
REVERT: B   98 MET cc_start: 0.9354 (ttt) cc_final: 0.9005 (ttt)
REVERT: B  100 MET cc_start: 0.9559 (ttp) cc_final: 0.9196 (tmm)
REVERT: B  108 MET cc_start: 0.9537 (mtm) cc_final: 0.9125 (mtp)
REVERT: B  111 MET cc_start: 0.9341 (ttp) cc_final: 0.8589 (ppp)
REVERT: B  115 PHE cc_start: 0.8916 (t80) cc_final: 0.8510 (t80)
REVERT: B  124 LEU cc_start: 0.9337 (tp) cc_final: 0.9052 (tp)
REVERT: B  149 GLU cc_start: 0.9042 (mp0) cc_final: 0.8683 (mp0)
REVERT: B  200 MET cc_start: 0.9414 (tmm) cc_final: 0.9060 (tmm)
REVERT: B  210 MET cc_start: 0.8719 (tpt) cc_final: 0.8428 (tpp)
REVERT: B  242 MET cc_start: 0.9009 (mmm) cc_final: 0.8773 (mmm)
REVERT: B  244 MET cc_start: 0.9310 (ppp) cc_final: 0.8908 (ppp)
REVERT: B  527 GLN cc_start: 0.9363 (pt0) cc_final: 0.9129 (pp30)
REVERT: B  538 ARG cc_start: 0.8444 (tpm170) cc_final: 0.8181 (tpp-160)
REVERT: A   98 MET cc_start: 0.9236 (tpp) cc_final: 0.8865 (tpp)
REVERT: A  109 MET cc_start: 0.8984 (mmp) cc_final: 0.8265 (tmm)
REVERT: A  115 PHE cc_start: 0.8978 (t80) cc_final: 0.8705 (t80)
REVERT: A  116 PHE cc_start: 0.9025 (m-80) cc_final: 0.8504 (m-80)
REVERT: A  160 MET cc_start: 0.9368 (mmm) cc_final: 0.9053 (mmm)
REVERT: A  174 LEU cc_start: 0.9338 (mt) cc_final: 0.9083 (mt)
REVERT: A  200 MET cc_start: 0.9446 (tmm) cc_final: 0.9138 (tmm)
REVERT: A  210 MET cc_start: 0.8829 (mmt) cc_final: 0.8300 (mmm)
REVERT: A  244 MET cc_start: 0.9370 (ppp) cc_final: 0.9027 (ppp)
REVERT: A  392 PHE cc_start: 0.9328 (m-10) cc_final: 0.8938 (m-10)
REVERT: A  437 ILE cc_start: 0.9472 (tt) cc_final: 0.9219 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 240
  average time/residue: 0.1581
  time to fit residues: 55.4670
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  : 0.956 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 100 optimal weight:    6.9990
   chunk 57 optimal weight:    0.9980
   chunk 104 optimal weight:    5.9990
   chunk 40 optimal weight:    7.9990
   chunk 70 optimal weight:    1.9990
   chunk 74 optimal weight:    4.9990
   chunk 71 optimal weight:    0.7980
   chunk 59 optimal weight:    2.9990
   chunk 30 optimal weight:    5.9990
   chunk 67 optimal weight:    2.9990
   overall best weight:    1.5586

-------------------------------------------------------------------------------
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 214 HIS
** A 436 ASN ** 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 = 0.3419 r_free = 0.3419 target = 0.075464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.055083 restraints weight = 34179.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.057362 restraints weight = 21078.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.059042 restraints weight = 14780.327|
|-----------------------------------------------------------------------------|
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.3957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   8950  Z= 0.159
  Angle     :  0.610   7.258  12092  Z= 0.323
  Chirality :  0.042   0.272   1440
  Planarity :  0.004   0.049   1532
  Dihedral  :  4.639  19.715   1238
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 13.97
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.38 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  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:  1.47 (0.19), residues: 726
  sheet:  0.18 (0.89), residues: 32
  loop : -1.25 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A  66 
 HIS   0.002   0.000   HIS A 576 
 PHE   0.013   0.001   PHE B 105 
 TYR   0.012   0.001   TYR B 410 
 ARG   0.003   0.000   ARG B 236 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04395 (  557)
  hydrogen bonds       : angle       4.72533 ( 1656)
  covalent geometry    : bond        0.00326 ( 8950)
  covalent geometry    : angle       0.61047 (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
  243 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 243
  time to evaluate  : 1.183 
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: 0.9168 (mt) cc_final: 0.8952 (mt)
REVERT: B   98 MET cc_start: 0.9370 (ttt) cc_final: 0.8997 (ttt)
REVERT: B  100 MET cc_start: 0.9587 (ttp) cc_final: 0.9242 (tmm)
REVERT: B  108 MET cc_start: 0.9543 (mtm) cc_final: 0.9225 (mtp)
REVERT: B  115 PHE cc_start: 0.8931 (t80) cc_final: 0.8558 (t80)
REVERT: B  149 GLU cc_start: 0.9055 (mp0) cc_final: 0.8702 (mp0)
REVERT: B  200 MET cc_start: 0.9425 (tmm) cc_final: 0.9065 (tmm)
REVERT: B  203 VAL cc_start: 0.9423 (t) cc_final: 0.9179 (p)
REVERT: B  210 MET cc_start: 0.8806 (tpt) cc_final: 0.8181 (tpp)
REVERT: B  229 ARG cc_start: 0.9207 (ttm-80) cc_final: 0.8832 (ttm-80)
REVERT: B  242 MET cc_start: 0.9009 (mmm) cc_final: 0.8771 (mmm)
REVERT: B  244 MET cc_start: 0.9323 (ppp) cc_final: 0.8918 (ppp)
REVERT: B  332 LYS cc_start: 0.9678 (mttt) cc_final: 0.9419 (mmtt)
REVERT: B  402 MET cc_start: 0.8824 (tmm) cc_final: 0.8592 (tmm)
REVERT: B  456 MET cc_start: 0.9256 (mpp) cc_final: 0.9039 (mmp)
REVERT: B  538 ARG cc_start: 0.8486 (tpm170) cc_final: 0.8138 (tpm170)
REVERT: A  115 PHE cc_start: 0.9000 (t80) cc_final: 0.8651 (t80)
REVERT: A  116 PHE cc_start: 0.8947 (m-80) cc_final: 0.8374 (m-80)
REVERT: A  160 MET cc_start: 0.9378 (mmm) cc_final: 0.9087 (mmm)
REVERT: A  200 MET cc_start: 0.9455 (tmm) cc_final: 0.9147 (tmm)
REVERT: A  210 MET cc_start: 0.8795 (mmt) cc_final: 0.8296 (mmm)
REVERT: A  244 MET cc_start: 0.9375 (ppp) cc_final: 0.9034 (ppp)
REVERT: A  390 THR cc_start: 0.9026 (p) cc_final: 0.8709 (p)
REVERT: A  392 PHE cc_start: 0.9330 (m-10) cc_final: 0.8979 (m-10)
REVERT: A  437 ILE cc_start: 0.9496 (tt) cc_final: 0.9252 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 243
  average time/residue: 0.1688
  time to fit residues: 59.4003
Evaluate side-chains
  199 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 96 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9980
   chunk 43 optimal weight:    0.6980
   chunk 102 optimal weight:    0.4980
   chunk 99 optimal weight:    5.9990
   chunk 37 optimal weight:    0.0770
   chunk 86 optimal weight:    0.8980
   chunk 41 optimal weight:    0.3980
   chunk 49 optimal weight:    7.9990
   overall best weight:    0.5138

-------------------------------------------------------------------------------
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 = 0.3466 r_free = 0.3466 target = 0.078223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.057632 restraints weight = 33367.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.059991 restraints weight = 20684.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.061772 restraints weight = 14576.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.4159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   8950  Z= 0.127
  Angle     :  0.604   6.481  12092  Z= 0.315
  Chirality :  0.043   0.308   1440
  Planarity :  0.004   0.049   1532
  Dihedral  :  4.560  27.703   1238
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 12.85
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.94 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  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:  0.93 (0.26), residues: 1134
  helix:  1.50 (0.19), residues: 730
  sheet:  0.48 (0.90), residues: 32
  loop : -1.16 (0.34), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A  66 
 HIS   0.004   0.001   HIS A 214 
 PHE   0.023   0.001   PHE B 157 
 TYR   0.017   0.002   TYR A 130 
 ARG   0.003   0.000   ARG B 236 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04071 (  557)
  hydrogen bonds       : angle       4.57376 ( 1656)
  covalent geometry    : bond        0.00265 ( 8950)
  covalent geometry    : angle       0.60382 (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
  238 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 238
  time to evaluate  : 0.973 
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: 0.9134 (mt) cc_final: 0.8925 (mt)
REVERT: B   98 MET cc_start: 0.9354 (ttt) cc_final: 0.9003 (ttt)
REVERT: B  100 MET cc_start: 0.9566 (ttp) cc_final: 0.9217 (tmm)
REVERT: B  108 MET cc_start: 0.9465 (mtm) cc_final: 0.8917 (mtp)
REVERT: B  111 MET cc_start: 0.9010 (ttp) cc_final: 0.8797 (ppp)
REVERT: B  200 MET cc_start: 0.9435 (tmm) cc_final: 0.9066 (tmm)
REVERT: B  203 VAL cc_start: 0.9378 (t) cc_final: 0.9139 (p)
REVERT: B  210 MET cc_start: 0.8667 (tpt) cc_final: 0.8394 (tpp)
REVERT: B  237 MET cc_start: 0.8878 (ptm) cc_final: 0.8556 (ppp)
REVERT: B  244 MET cc_start: 0.9304 (ppp) cc_final: 0.8900 (ppp)
REVERT: B  332 LYS cc_start: 0.9687 (mttt) cc_final: 0.9403 (mmtt)
REVERT: B  410 TYR cc_start: 0.7784 (m-80) cc_final: 0.6928 (m-80)
REVERT: B  456 MET cc_start: 0.9210 (mpp) cc_final: 0.8987 (mmp)
REVERT: B  527 GLN cc_start: 0.9329 (pt0) cc_final: 0.9091 (pp30)
REVERT: B  538 ARG cc_start: 0.8457 (tpm170) cc_final: 0.8089 (tpp-160)
REVERT: A   98 MET cc_start: 0.9218 (tpp) cc_final: 0.8586 (tpp)
REVERT: A  105 PHE cc_start: 0.9422 (t80) cc_final: 0.9076 (t80)
REVERT: A  109 MET cc_start: 0.8911 (mmp) cc_final: 0.7875 (tmm)
REVERT: A  115 PHE cc_start: 0.8997 (t80) cc_final: 0.8675 (t80)
REVERT: A  116 PHE cc_start: 0.8929 (m-80) cc_final: 0.8404 (m-80)
REVERT: A  149 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8773 (mm-30)
REVERT: A  160 MET cc_start: 0.9377 (mmm) cc_final: 0.9074 (mmm)
REVERT: A  180 ILE cc_start: 0.9038 (tt) cc_final: 0.8836 (pt)
REVERT: A  200 MET cc_start: 0.9446 (tmm) cc_final: 0.9137 (tmm)
REVERT: A  210 MET cc_start: 0.8810 (mmt) cc_final: 0.8295 (mmm)
REVERT: A  244 MET cc_start: 0.9354 (ppp) cc_final: 0.9011 (ppp)
REVERT: A  315 CYS cc_start: 0.8974 (t) cc_final: 0.8769 (t)
REVERT: A  390 THR cc_start: 0.9093 (p) cc_final: 0.8763 (p)
REVERT: A  392 PHE cc_start: 0.9287 (m-10) cc_final: 0.8919 (m-10)
REVERT: A  410 TYR cc_start: 0.8237 (m-10) cc_final: 0.7779 (m-80)
REVERT: A  437 ILE cc_start: 0.9461 (tt) cc_final: 0.9200 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 238
  average time/residue: 0.1648
  time to fit residues: 56.8092
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  : 0.957 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 3 optimal weight:    0.1980
   chunk 78 optimal weight:    0.6980
   chunk 6 optimal weight:    0.5980
   chunk 79 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 87 optimal weight:    0.8980
   chunk 77 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 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 = 0.3477 r_free = 0.3477 target = 0.078565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.057823 restraints weight = 33149.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.060196 restraints weight = 20821.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.061954 restraints weight = 14757.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.4318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   8950  Z= 0.126
  Angle     :  0.611   6.899  12092  Z= 0.318
  Chirality :  0.043   0.271   1440
  Planarity :  0.004   0.048   1532
  Dihedral  :  4.484  25.459   1238
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 13.18
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.85 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  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:  0.92 (0.26), residues: 1134
  helix:  1.50 (0.19), residues: 734
  sheet: -0.39 (0.76), residues: 46
  loop : -1.13 (0.35), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  66 
 HIS   0.002   0.000   HIS B 214 
 PHE   0.021   0.001   PHE B 157 
 TYR   0.015   0.001   TYR A 130 
 ARG   0.005   0.000   ARG A  14 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04041 (  557)
  hydrogen bonds       : angle       4.54573 ( 1656)
  covalent geometry    : bond        0.00266 ( 8950)
  covalent geometry    : angle       0.61075 (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
  240 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 240
  time to evaluate  : 1.011 
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: 0.9150 (mt) cc_final: 0.8941 (mt)
REVERT: B   98 MET cc_start: 0.9337 (ttt) cc_final: 0.9011 (ttt)
REVERT: B  100 MET cc_start: 0.9562 (ttp) cc_final: 0.9200 (tmm)
REVERT: B  108 MET cc_start: 0.9366 (mtm) cc_final: 0.9077 (mtp)
REVERT: B  200 MET cc_start: 0.9442 (tmm) cc_final: 0.9072 (tmm)
REVERT: B  203 VAL cc_start: 0.9388 (t) cc_final: 0.9169 (p)
REVERT: B  208 GLU cc_start: 0.9163 (mp0) cc_final: 0.8878 (mp0)
REVERT: B  210 MET cc_start: 0.8744 (tpt) cc_final: 0.8286 (tpp)
REVERT: B  237 MET cc_start: 0.8889 (ptm) cc_final: 0.8575 (ppp)
REVERT: B  244 MET cc_start: 0.9308 (ppp) cc_final: 0.8906 (ppp)
REVERT: B  312 MET cc_start: 0.8386 (ttt) cc_final: 0.7671 (mmm)
REVERT: B  315 CYS cc_start: 0.8205 (m) cc_final: 0.7938 (m)
REVERT: B  456 MET cc_start: 0.9208 (mpp) cc_final: 0.8998 (mmp)
REVERT: B  480 LEU cc_start: 0.9700 (tt) cc_final: 0.9428 (mm)
REVERT: B  503 ILE cc_start: 0.9743 (mm) cc_final: 0.9489 (tp)
REVERT: B  527 GLN cc_start: 0.9308 (pt0) cc_final: 0.9070 (pp30)
REVERT: B  538 ARG cc_start: 0.8469 (tpm170) cc_final: 0.8100 (tpp-160)
REVERT: A   98 MET cc_start: 0.9027 (ttm) cc_final: 0.8717 (tpp)
REVERT: A  109 MET cc_start: 0.8555 (mmp) cc_final: 0.7513 (tmm)
REVERT: A  115 PHE cc_start: 0.8987 (t80) cc_final: 0.8707 (t80)
REVERT: A  116 PHE cc_start: 0.8951 (m-80) cc_final: 0.8459 (m-80)
REVERT: A  156 LEU cc_start: 0.9684 (mt) cc_final: 0.9448 (mt)
REVERT: A  160 MET cc_start: 0.9359 (mmm) cc_final: 0.9085 (mmm)
REVERT: A  180 ILE cc_start: 0.9017 (tt) cc_final: 0.8815 (pt)
REVERT: A  196 MET cc_start: 0.8892 (mmp) cc_final: 0.8236 (mmt)
REVERT: A  200 MET cc_start: 0.9433 (tmm) cc_final: 0.9118 (tmm)
REVERT: A  210 MET cc_start: 0.8851 (mmt) cc_final: 0.8291 (mmm)
REVERT: A  244 MET cc_start: 0.9354 (ppp) cc_final: 0.8955 (ppp)
REVERT: A  312 MET cc_start: 0.8191 (mmm) cc_final: 0.7418 (mmm)
REVERT: A  315 CYS cc_start: 0.9005 (t) cc_final: 0.8414 (p)
REVERT: A  390 THR cc_start: 0.9078 (p) cc_final: 0.8776 (p)
REVERT: A  392 PHE cc_start: 0.9266 (m-10) cc_final: 0.8908 (m-10)
REVERT: A  410 TYR cc_start: 0.8220 (m-10) cc_final: 0.7764 (m-80)
REVERT: A  437 ILE cc_start: 0.9464 (tt) cc_final: 0.9221 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 240
  average time/residue: 0.1729
  time to fit residues: 60.1611
Evaluate side-chains
  203 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 1.037 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 95 optimal weight:    0.9980
   chunk 72 optimal weight:    0.5980
   chunk 70 optimal weight:    0.7980
   chunk 87 optimal weight:    4.9990
   chunk 15 optimal weight:    0.5980
   chunk 73 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   chunk 88 optimal weight:    6.9990
   chunk 100 optimal weight:    6.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 436 ASN ** 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 = 0.3477 r_free = 0.3477 target = 0.078619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.057728 restraints weight = 33596.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.060078 restraints weight = 21256.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.061821 restraints weight = 15124.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.4485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   8950  Z= 0.128
  Angle     :  0.625   9.131  12092  Z= 0.323
  Chirality :  0.043   0.269   1440
  Planarity :  0.004   0.047   1532
  Dihedral  :  4.466  25.677   1238
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 13.52
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.11 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  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:  0.97 (0.26), residues: 1134
  helix:  1.55 (0.19), residues: 734
  sheet: -0.23 (0.74), residues: 48
  loop : -1.17 (0.35), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  66 
 HIS   0.003   0.000   HIS A 107 
 PHE   0.038   0.002   PHE B 115 
 TYR   0.021   0.002   TYR A 130 
 ARG   0.005   0.000   ARG B 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03969 (  557)
  hydrogen bonds       : angle       4.53352 ( 1656)
  covalent geometry    : bond        0.00273 ( 8950)
  covalent geometry    : angle       0.62495 (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
  231 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 231
  time to evaluate  : 0.982 
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: 0.9134 (mt) cc_final: 0.8927 (mt)
REVERT: B   98 MET cc_start: 0.9354 (ttt) cc_final: 0.9007 (ttt)
REVERT: B  100 MET cc_start: 0.9549 (ttp) cc_final: 0.9181 (tmm)
REVERT: B  108 MET cc_start: 0.9366 (mtm) cc_final: 0.9061 (mtp)
REVERT: B  200 MET cc_start: 0.9456 (tmm) cc_final: 0.9084 (tmm)
REVERT: B  203 VAL cc_start: 0.9406 (t) cc_final: 0.9164 (p)
REVERT: B  210 MET cc_start: 0.8771 (tpt) cc_final: 0.8074 (tpp)
REVERT: B  229 ARG cc_start: 0.9204 (ttm-80) cc_final: 0.8883 (ttm-80)
REVERT: B  237 MET cc_start: 0.8860 (ptm) cc_final: 0.8570 (ppp)
REVERT: B  244 MET cc_start: 0.9313 (ppp) cc_final: 0.8973 (ppp)
REVERT: B  312 MET cc_start: 0.8346 (ttt) cc_final: 0.7649 (mmm)
REVERT: B  315 CYS cc_start: 0.8190 (m) cc_final: 0.7934 (m)
REVERT: B  456 MET cc_start: 0.9215 (mpp) cc_final: 0.9002 (mmp)
REVERT: B  480 LEU cc_start: 0.9691 (tt) cc_final: 0.9418 (mm)
REVERT: B  503 ILE cc_start: 0.9741 (mm) cc_final: 0.9497 (tp)
REVERT: B  538 ARG cc_start: 0.8486 (tpm170) cc_final: 0.8101 (tpp-160)
REVERT: A   67 MET cc_start: 0.8529 (mmp) cc_final: 0.8271 (mmp)
REVERT: A   98 MET cc_start: 0.8978 (ttm) cc_final: 0.8731 (tpp)
REVERT: A  109 MET cc_start: 0.8438 (mmp) cc_final: 0.7865 (tmm)
REVERT: A  115 PHE cc_start: 0.8996 (t80) cc_final: 0.8679 (t80)
REVERT: A  156 LEU cc_start: 0.9690 (mt) cc_final: 0.9483 (mt)
REVERT: A  160 MET cc_start: 0.9373 (mmm) cc_final: 0.9078 (mmm)
REVERT: A  196 MET cc_start: 0.8884 (mmp) cc_final: 0.8220 (mmt)
REVERT: A  200 MET cc_start: 0.9433 (tmm) cc_final: 0.9123 (tmm)
REVERT: A  210 MET cc_start: 0.8854 (mmt) cc_final: 0.8353 (mmm)
REVERT: A  244 MET cc_start: 0.9340 (ppp) cc_final: 0.8941 (ppp)
REVERT: A  291 MET cc_start: 0.9390 (tpt) cc_final: 0.9168 (tpp)
REVERT: A  312 MET cc_start: 0.8122 (mmm) cc_final: 0.7682 (mmm)
REVERT: A  315 CYS cc_start: 0.9034 (t) cc_final: 0.8829 (t)
REVERT: A  390 THR cc_start: 0.9086 (p) cc_final: 0.8778 (p)
REVERT: A  392 PHE cc_start: 0.9250 (m-10) cc_final: 0.8887 (m-10)
REVERT: A  410 TYR cc_start: 0.8214 (m-10) cc_final: 0.7765 (m-80)
REVERT: A  437 ILE cc_start: 0.9477 (tt) cc_final: 0.9243 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 231
  average time/residue: 0.1618
  time to fit residues: 55.1440
Evaluate side-chains
  202 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 37 optimal weight:    4.9990
   chunk 12 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   chunk 53 optimal weight:    6.9990
   chunk 86 optimal weight:    0.0670
   chunk 54 optimal weight:    9.9990
   chunk 111 optimal weight:    5.9990
   chunk 102 optimal weight:    9.9990
   chunk 84 optimal weight:    0.6980
   chunk 87 optimal weight:    5.9990
   overall best weight:    0.7322

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

Flipped N/Q/H residues before XYZ refinement:
A 134 GLN
** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 520 GLN
** A 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 574 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.078641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.057776 restraints weight = 33299.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.060131 restraints weight = 20948.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.061917 restraints weight = 14922.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.4609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   8950  Z= 0.127
  Angle     :  0.624   9.053  12092  Z= 0.323
  Chirality :  0.043   0.255   1440
  Planarity :  0.004   0.046   1532
  Dihedral  :  4.430  26.635   1238
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 13.24
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.85 %
    Favored  : 94.80 %
  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:  0.98 (0.26), residues: 1134
  helix:  1.59 (0.19), residues: 732
  sheet: -0.25 (0.77), residues: 46
  loop : -1.22 (0.35), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A  66 
 HIS   0.007   0.001   HIS A 214 
 PHE   0.026   0.001   PHE A 105 
 TYR   0.029   0.002   TYR A 130 
 ARG   0.005   0.000   ARG B 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03946 (  557)
  hydrogen bonds       : angle       4.52413 ( 1656)
  covalent geometry    : bond        0.00274 ( 8950)
  covalent geometry    : angle       0.62397 (12092)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3629.75 seconds
wall clock time: 64 minutes 1.61 seconds (3841.61 seconds total)