Starting phenix.real_space_refine
on Thu Mar 13 00:12:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yfw_39231/03_2025/8yfw_39231.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yfw_39231/03_2025/8yfw_39231.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yfw_39231/03_2025/8yfw_39231.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yfw_39231/03_2025/8yfw_39231.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yfw_39231/03_2025/8yfw_39231.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yfw_39231/03_2025/8yfw_39231.cif"
  }
  resolution = 3.65
  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=   0.056
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      32      5.16       5
     C    5511      2.51       5
     N    1423      2.21       5
     O    1453      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 59 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8419
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4222
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 583, 4222
          Classifications: {'peptide': 583}
          Incomplete info: {'truncation_to_alanine': 168}
          Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 562}
          Chain breaks: 1
          Unresolved chain link angles: 4
          Unresolved non-hydrogen bonds: 647
          Unresolved non-hydrogen angles: 817
          Unresolved non-hydrogen dihedrals: 541
          Unresolved non-hydrogen chiralities: 46
          Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 4, 'TYR:plan': 7, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 12, 'GLU:plan': 20, 'ARG:plan': 11}
          Unresolved non-hydrogen planarities: 391
    Chain: "B"
      Number of atoms: 4197
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 578, 4197
          Classifications: {'peptide': 578}
          Incomplete info: {'truncation_to_alanine': 164}
          Link IDs: {'PTRANS': 19, 'TRANS': 558}
          Chain breaks: 1
          Unresolved chain link angles: 4
          Unresolved non-hydrogen bonds: 624
          Unresolved non-hydrogen angles: 787
          Unresolved non-hydrogen dihedrals: 520
          Unresolved non-hydrogen chiralities: 46
          Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 11, 'GLU:plan': 19, 'ARG:plan': 11}
          Unresolved non-hydrogen planarities: 370
  Time building chain proxies: 5.29, per 1000 atoms: 0.63
  Number of scatterers: 8419
  At special positions: 0
  Unit cell: (121, 127.6, 127.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      32     16.00
     O    1453      8.00
     N    1423      7.00
     C    5511      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 415 " - pdb=" SG  CYS A 440 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 415 " - pdb=" SG  CYS B 440 " distance=2.03

  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: 2.17
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2230

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 0 sheets defined
      78.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.68
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 36
    Processing helix  chain 'A' and resid 43 through 100
    Processing helix  chain 'A' and resid 119 through 168
    Processing helix  chain 'A' and resid 170 through 180
      removed outlier: 3.533A  pdb=" N   ASP A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 188
    Processing helix  chain 'A' and resid 189 through 206
      removed outlier: 3.847A  pdb=" N   GLN A 193 " --> pdb=" O   LYS A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 218
    Processing helix  chain 'A' and resid 230 through 258
      removed outlier: 3.910A  pdb=" N   THR A 234 " --> pdb=" O   PRO A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 295
      removed outlier: 3.551A  pdb=" N   ILE A 269 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 4.899A  pdb=" N   GLY A 274 " --> pdb=" O   ARG A 270 " (cutoff:3.500A)
      removed outlier: 5.046A  pdb=" N   GLY A 275 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 337
      removed outlier: 3.548A  pdb=" N   LEU A 316 " --> pdb=" O   SER A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 360
    Processing helix  chain 'A' and resid 367 through 383
    Processing helix  chain 'A' and resid 390 through 402
      removed outlier: 3.748A  pdb=" N   PHE A 394 " --> pdb=" O   GLY A 390 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   SER A 402 " --> pdb=" O   ASP A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 419
      removed outlier: 4.058A  pdb=" N   LEU A 407 " --> pdb=" O   LEU A 403 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   LEU A 419 " --> pdb=" O   CYS A 415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 471
      removed outlier: 4.311A  pdb=" N   ILE A 450 " --> pdb=" O   GLY A 446 " (cutoff:3.500A)
      Proline residue:  A 455  - end of helix
    Processing helix  chain 'A' and resid 476 through 500
      removed outlier: 4.253A  pdb=" N   THR A 486 " --> pdb=" O   LYS A 482 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   PHE A 487 " --> pdb=" O   TYR A 483 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   PHE A 488 " --> pdb=" O   SER A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 532
      removed outlier: 4.069A  pdb=" N   PHE A 510 " --> pdb=" O   ASP A 506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 570
      removed outlier: 4.081A  pdb=" N   TYR A 559 " --> pdb=" O   GLN A 555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 571 through 581
      removed outlier: 3.970A  pdb=" N   ILE A 575 " --> pdb=" O   PHE A 571 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ILE A 579 " --> pdb=" O   ILE A 575 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   THR A 580 " --> pdb=" O   GLN A 576 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 597
      removed outlier: 3.944A  pdb=" N   ILE A 592 " --> pdb=" O   SER A 588 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 599 through 616
      removed outlier: 3.798A  pdb=" N   PHE A 609 " --> pdb=" O   PHE A 605 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   PHE A 610 " --> pdb=" O   VAL A 606 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   LEU A 612 " --> pdb=" O   ASN A 608 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   GLU A 613 " --> pdb=" O   PHE A 609 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 27 through 36
      removed outlier: 3.583A  pdb=" N   GLN B  33 " --> pdb=" O   LEU B  29 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   ALA B  36 " --> pdb=" O   ALA B  32 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 43 through 100
      removed outlier: 3.804A  pdb=" N   VAL B  47 " --> pdb=" O   ASP B  43 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 168
    Processing helix  chain 'B' and resid 170 through 179
    Processing helix  chain 'B' and resid 183 through 188
      removed outlier: 3.795A  pdb=" N   THR B 187 " --> pdb=" O   ALA B 183 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 206
      removed outlier: 3.888A  pdb=" N   GLN B 193 " --> pdb=" O   LYS B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 210 through 218
    Processing helix  chain 'B' and resid 230 through 258
      removed outlier: 3.559A  pdb=" N   THR B 234 " --> pdb=" O   PRO B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 265 through 296
      removed outlier: 4.373A  pdb=" N   GLY B 274 " --> pdb=" O   ARG B 270 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   GLY B 275 " --> pdb=" O   ILE B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 303
      removed outlier: 3.552A  pdb=" N   ILE B 302 " --> pdb=" O   ASN B 298 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 312 through 337
    Processing helix  chain 'B' and resid 346 through 360
      removed outlier: 3.609A  pdb=" N   ALA B 350 " --> pdb=" O   VAL B 346 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   LEU B 351 " --> pdb=" O   TYR B 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 384
      removed outlier: 3.630A  pdb=" N   PHE B 372 " --> pdb=" O   TYR B 368 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   THR B 383 " --> pdb=" O   PHE B 379 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   ALA B 384 " --> pdb=" O   ARG B 380 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 390 through 403
      removed outlier: 3.597A  pdb=" N   SER B 402 " --> pdb=" O   ASP B 398 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 420
      removed outlier: 3.801A  pdb=" N   MET B 408 " --> pdb=" O   SER B 404 " (cutoff:3.500A)
      removed outlier: 4.913A  pdb=" N   LEU B 410 " --> pdb=" O   ILE B 406 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   GLU B 411 " --> pdb=" O   LEU B 407 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 445 through 471
      removed outlier: 4.511A  pdb=" N   ALA B 449 " --> pdb=" O   TYR B 445 " (cutoff:3.500A)
      Proline residue:  B 455  - end of helix
    Processing helix  chain 'B' and resid 473 through 501
      removed outlier: 4.306A  pdb=" N   THR B 486 " --> pdb=" O   LYS B 482 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   PHE B 487 " --> pdb=" O   TYR B 483 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   GLU B 501 " --> pdb=" O   SER B 497 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 532
      removed outlier: 4.413A  pdb=" N   TYR B 512 " --> pdb=" O   MET B 508 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ILE B 515 " --> pdb=" O   PHE B 511 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   VAL B 516 " --> pdb=" O   TYR B 512 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ILE B 519 " --> pdb=" O   ILE B 515 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   SER B 521 " --> pdb=" O   PHE B 517 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   TYR B 524 " --> pdb=" O   ILE B 520 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   MET B 532 " --> pdb=" O   TRP B 528 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 555 through 571
      removed outlier: 4.035A  pdb=" N   TYR B 559 " --> pdb=" O   GLN B 555 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   PHE B 571 " --> pdb=" O   VAL B 567 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 572 through 580
      removed outlier: 3.967A  pdb=" N   GLN B 576 " --> pdb=" O   ALA B 572 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 590 through 620
      Proline residue:  B 598  - end of helix
      removed outlier: 3.811A  pdb=" N   VAL B 601 " --> pdb=" O   ALA B 597 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   VAL B 606 " --> pdb=" O   PHE B 602 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   PHE B 609 " --> pdb=" O   PHE B 605 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   PHE B 610 " --> pdb=" O   VAL B 606 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LEU B 612 " --> pdb=" O   ASN B 608 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLU B 613 " --> pdb=" O   PHE B 609 " (cutoff:3.500A)

    667 hydrogen bonds defined for protein.
    2001 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: 2.26

  Time building geometry restraints manager: 2.59 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2684
        1.34 -     1.46: 2048
        1.46 -     1.58: 3861
        1.58 -     1.70: 0
        1.70 -     1.81: 44
  Bond restraints: 8637
  Sorted by residual:
  bond pdb=" CB  CYS B 415 "
       pdb=" SG  CYS B 415 "
    ideal  model  delta    sigma   weight residual
    1.808  1.733  0.075 3.30e-02 9.18e+02 5.19e+00
  bond pdb=" CB  CYS B 440 "
       pdb=" SG  CYS B 440 "
    ideal  model  delta    sigma   weight residual
    1.808  1.743  0.065 3.30e-02 9.18e+02 3.93e+00
  bond pdb=" CB  PRO B 307 "
       pdb=" CG  PRO B 307 "
    ideal  model  delta    sigma   weight residual
    1.492  1.577 -0.085 5.00e-02 4.00e+02 2.87e+00
  bond pdb=" CB  PRO B 343 "
       pdb=" CG  PRO B 343 "
    ideal  model  delta    sigma   weight residual
    1.492  1.561 -0.069 5.00e-02 4.00e+02 1.93e+00
  bond pdb=" CB  PRO B 586 "
       pdb=" CG  PRO B 586 "
    ideal  model  delta    sigma   weight residual
    1.492  1.557 -0.065 5.00e-02 4.00e+02 1.67e+00
  ... (remaining 8632 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.99: 11762
        3.99 -     7.97: 57
        7.97 -    11.96: 3
       11.96 -    15.94: 0
       15.94 -    19.93: 1
  Bond angle restraints: 11823
  Sorted by residual:
  angle pdb=" C   ALA A 226 "
        pdb=" N   GLN A 227 "
        pdb=" CA  GLN A 227 "
      ideal   model   delta    sigma   weight residual
     121.70  141.63  -19.93 1.80e+00 3.09e-01 1.23e+02
  angle pdb=" C   SER B 340 "
        pdb=" CA  SER B 340 "
        pdb=" CB  SER B 340 "
      ideal   model   delta    sigma   weight residual
     116.54  110.08    6.46 1.15e+00 7.56e-01 3.16e+01
  angle pdb=" CA  PRO B 307 "
        pdb=" N   PRO B 307 "
        pdb=" CD  PRO B 307 "
      ideal   model   delta    sigma   weight residual
     112.00  104.68    7.32 1.40e+00 5.10e-01 2.74e+01
  angle pdb=" C   ILE A 454 "
        pdb=" CA  ILE A 454 "
        pdb=" CB  ILE A 454 "
      ideal   model   delta    sigma   weight residual
     113.70  109.08    4.62 9.50e-01 1.11e+00 2.37e+01
  angle pdb=" C   THR B 383 "
        pdb=" N   ALA B 384 "
        pdb=" CA  ALA B 384 "
      ideal   model   delta    sigma   weight residual
     121.80  131.66   -9.86 2.44e+00 1.68e-01 1.63e+01
  ... (remaining 11818 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.52: 4365
       17.52 -    35.04: 455
       35.04 -    52.56: 112
       52.56 -    70.07: 15
       70.07 -    87.59: 8
  Dihedral angle restraints: 4955
    sinusoidal: 1526
      harmonic: 3429
  Sorted by residual:
  dihedral pdb=" CB  CYS B 415 "
           pdb=" SG  CYS B 415 "
           pdb=" SG  CYS B 440 "
           pdb=" CB  CYS B 440 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  178.72  -85.72     1      1.00e+01 1.00e-02 8.88e+01
  dihedral pdb=" CB  CYS A 415 "
           pdb=" SG  CYS A 415 "
           pdb=" SG  CYS A 440 "
           pdb=" CB  CYS A 440 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  159.03  -66.03     1      1.00e+01 1.00e-02 5.70e+01
  dihedral pdb=" CA  CYS A 440 "
           pdb=" C   CYS A 440 "
           pdb=" N   HIS A 441 "
           pdb=" CA  HIS A 441 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.36   27.64     0      5.00e+00 4.00e-02 3.05e+01
  ... (remaining 4952 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 1152
       0.053 -    0.107: 195
       0.107 -    0.160: 24
       0.160 -    0.213: 3
       0.213 -    0.266: 1
  Chirality restraints: 1375
  Sorted by residual:
  chirality pdb=" CB  ILE B 271 "
            pdb=" CA  ILE B 271 "
            pdb=" CG1 ILE B 271 "
            pdb=" CG2 ILE B 271 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.27 2.00e-01 2.50e+01 1.77e+00
  chirality pdb=" CA  CYS A 440 "
            pdb=" N   CYS A 440 "
            pdb=" C   CYS A 440 "
            pdb=" CB  CYS A 440 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.80e-01
  chirality pdb=" CG  LEU B 284 "
            pdb=" CB  LEU B 284 "
            pdb=" CD1 LEU B 284 "
            pdb=" CD2 LEU B 284 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.41   -0.18 2.00e-01 2.50e+01 7.67e-01
  ... (remaining 1372 not shown)

  Planarity restraints: 1499
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 306 "   -0.113 5.00e-02 4.00e+02   1.68e-01 4.51e+01
        pdb=" N   PRO B 307 "    0.290 5.00e-02 4.00e+02
        pdb=" CA  PRO B 307 "   -0.094 5.00e-02 4.00e+02
        pdb=" CD  PRO B 307 "   -0.083 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 585 "   -0.046 5.00e-02 4.00e+02   6.84e-02 7.50e+00
        pdb=" N   PRO B 586 "    0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO B 586 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO B 586 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 361 "   -0.042 5.00e-02 4.00e+02   6.37e-02 6.49e+00
        pdb=" N   PRO B 362 "    0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO B 362 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 362 "   -0.035 5.00e-02 4.00e+02
  ... (remaining 1496 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 214
        2.70 -     3.25: 9026
        3.25 -     3.80: 13801
        3.80 -     4.35: 15198
        4.35 -     4.90: 25311
  Nonbonded interactions: 63550
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 575 "
            pdb=" OG  SER A 578 "
     model   vdw
     2.152 3.040
  nonbonded pdb=" ND2 ASN B 288 "
            pdb=" OD1 ASN B 608 "
     model   vdw
     2.156 3.120
  nonbonded pdb=" OE1 GLU B 318 "
            pdb=" OH  TYR B 367 "
     model   vdw
     2.182 3.040
  nonbonded pdb=" OG  SER B 340 "
            pdb=" N   VAL B 341 "
     model   vdw
     2.183 3.120
  nonbonded pdb=" OD1 ASN B 618 "
            pdb=" N   ASN B 619 "
     model   vdw
     2.189 3.120
  ... (remaining 63545 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 26 through 620)
  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:             1.360
  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:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     21.760
  Find NCS groups from input model:        0.320
  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:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6990
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      :  0.004   0.085   8637  Z= 0.222
  Angle     :  0.737  19.928  11823  Z= 0.409
  Chirality :  0.041   0.266   1375
  Planarity :  0.006   0.168   1499
  Dihedral  : 15.862  87.593   2719
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 13.17
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.68 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  : 30.77 %
    Favored  : 68.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (0.26), residues: 1153
  helix:  2.18 (0.18), residues: 854
  sheet:  None (None), residues: 0
  loop : -2.16 (0.35), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP A 373 
 HIS   0.005   0.001   HIS A 299 
 PHE   0.028   0.002   PHE B 357 
 TYR   0.033   0.002   TYR B 412 
 ARG   0.007   0.001   ARG B 270 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 147
  time to evaluate  : 0.890 
Fit side-chains
REVERT: B  506 ASP cc_start: 0.6490 (t0) cc_final: 0.6279 (t0)
  outliers start: 2
  outliers final: 2
  residues processed: 148
  average time/residue: 0.1530
  time to fit residues: 34.0422
Evaluate side-chains
  145 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 143
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain B residue  416 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    2.9990
   chunk 87 optimal weight:    0.0020
   chunk 48 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   chunk 58 optimal weight:   50.0000
   chunk 46 optimal weight:    8.9990
   chunk 90 optimal weight:    4.9990
   chunk 34 optimal weight:    0.8980
   chunk 54 optimal weight:    0.0010
   chunk 67 optimal weight:   30.0000
   chunk 104 optimal weight:    5.9990
   overall best weight:    0.5196

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

Flipped N/Q/H residues before XYZ refinement:
B 576 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4636 r_free = 0.4636 target = 0.202966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.158872 restraints weight = 18176.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.157704 restraints weight = 13996.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.157280 restraints weight = 11394.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.4082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6993
moved from start:          0.0870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8637  Z= 0.186
  Angle     :  0.596   9.785  11823  Z= 0.320
  Chirality :  0.038   0.157   1375
  Planarity :  0.005   0.124   1499
  Dihedral  :  4.062  26.961   1242
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.99 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 23.08 %
    Favored  : 73.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.21 (0.25), residues: 1153
  helix:  2.50 (0.17), residues: 869
  sheet:  None (None), residues: 0
  loop : -2.07 (0.36), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 373 
 HIS   0.004   0.001   HIS A 299 
 PHE   0.025   0.001   PHE B 335 
 TYR   0.026   0.001   TYR B 412 
 ARG   0.005   0.001   ARG A 465 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 157
  time to evaluate  : 1.005 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 TYR cc_start: 0.7236 (t80) cc_final: 0.6861 (t80)
  outliers start: 25
  outliers final: 11
  residues processed: 169
  average time/residue: 0.1556
  time to fit residues: 38.8612
Evaluate side-chains
  151 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 140
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  288 ASN
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  310 ASN
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  396 LEU
Chi-restraints excluded: chain B residue  474 PHE
Chi-restraints excluded: chain B residue  499 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 62 optimal weight:   80.0000
   chunk 27 optimal weight:    3.9990
   chunk 65 optimal weight:    8.9990
   chunk 71 optimal weight:    0.3980
   chunk 91 optimal weight:    2.9990
   chunk 76 optimal weight:   20.0000
   chunk 87 optimal weight:    6.9990
   chunk 55 optimal weight:    2.9990
   chunk 3 optimal weight:   40.0000
   chunk 38 optimal weight:    4.9990
   overall best weight:    2.2788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4563 r_free = 0.4563 target = 0.195594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.153133 restraints weight = 18296.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.149361 restraints weight = 12817.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.150846 restraints weight = 10546.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.4020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7114
moved from start:          0.1778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   8637  Z= 0.352
  Angle     :  0.684   9.818  11823  Z= 0.367
  Chirality :  0.042   0.168   1375
  Planarity :  0.005   0.096   1499
  Dihedral  :  4.151  24.945   1239
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.51 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 23.36 %
    Favored  : 71.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.99 (0.25), residues: 1153
  helix:  2.32 (0.17), residues: 875
  sheet:  None (None), residues: 0
  loop : -2.16 (0.35), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP A 457 
 HIS   0.006   0.001   HIS B 313 
 PHE   0.029   0.002   PHE B 335 
 TYR   0.026   0.002   TYR B 412 
 ARG   0.008   0.001   ARG B 466 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 154
  time to evaluate  : 1.133 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 TYR cc_start: 0.7306 (t80) cc_final: 0.6788 (t80)
REVERT: A  585 LEU cc_start: 0.4522 (mt) cc_final: 0.4198 (tp)
REVERT: B  244 PHE cc_start: 0.7971 (t80) cc_final: 0.7355 (t80)
REVERT: B  495 LEU cc_start: 0.7719 (pp) cc_final: 0.7490 (pp)
  outliers start: 36
  outliers final: 21
  residues processed: 175
  average time/residue: 0.1657
  time to fit residues: 42.8352
Evaluate side-chains
  160 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 139
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain A residue  310 ASN
Chi-restraints excluded: chain A residue  336 PHE
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  576 GLN
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  381 VAL
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  396 LEU
Chi-restraints excluded: chain B residue  474 PHE
Chi-restraints excluded: chain B residue  496 TYR
Chi-restraints excluded: chain B residue  499 HIS
Chi-restraints excluded: chain B residue  591 ILE
Chi-restraints excluded: chain B residue  616 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 13 optimal weight:    8.9990
   chunk 112 optimal weight:    0.0030
   chunk 46 optimal weight:    7.9990
   chunk 41 optimal weight:    5.9990
   chunk 70 optimal weight:   20.0000
   chunk 71 optimal weight:   10.0000
   chunk 114 optimal weight:    0.8980
   chunk 82 optimal weight:    0.5980
   chunk 80 optimal weight:    0.5980
   chunk 88 optimal weight:    4.9990
   chunk 108 optimal weight:    4.9990
   overall best weight:    1.4192

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

Flipped N/Q/H residues before XYZ refinement:
A 288 ASN
B 499 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4581 r_free = 0.4581 target = 0.197307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.155576 restraints weight = 18123.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.151648 restraints weight = 12123.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.153293 restraints weight = 10267.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.4053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7068
moved from start:          0.2123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   8637  Z= 0.237
  Angle     :  0.598   9.635  11823  Z= 0.322
  Chirality :  0.039   0.141   1375
  Planarity :  0.004   0.088   1499
  Dihedral  :  4.019  22.942   1239
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.16 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 24.79 %
    Favored  : 70.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.21 (0.25), residues: 1153
  helix:  2.49 (0.17), residues: 875
  sheet:  None (None), residues: 0
  loop : -2.12 (0.35), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 373 
 HIS   0.004   0.001   HIS A 299 
 PHE   0.024   0.002   PHE A 511 
 TYR   0.046   0.002   TYR B 412 
 ARG   0.004   0.000   ARG B 270 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 156
  time to evaluate  : 0.899 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  290 TYR cc_start: 0.7097 (t80) cc_final: 0.6540 (t80)
REVERT: A  585 LEU cc_start: 0.4460 (mt) cc_final: 0.4190 (tp)
REVERT: B  244 PHE cc_start: 0.8035 (t80) cc_final: 0.7259 (t80)
REVERT: B  495 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7534 (pp)
  outliers start: 33
  outliers final: 23
  residues processed: 174
  average time/residue: 0.1606
  time to fit residues: 41.8110
Evaluate side-chains
  166 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 142
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  241 CYS
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  288 ASN
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  310 ASN
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  576 GLN
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  278 LEU
Chi-restraints excluded: chain B residue  279 ILE
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  396 LEU
Chi-restraints excluded: chain B residue  415 CYS
Chi-restraints excluded: chain B residue  474 PHE
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  496 TYR
Chi-restraints excluded: chain B residue  499 HIS
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  616 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 102 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 73 optimal weight:   10.0000
   chunk 18 optimal weight:    3.9990
   chunk 50 optimal weight:    5.9990
   chunk 43 optimal weight:    0.0370
   chunk 109 optimal weight:    0.0980
   chunk 59 optimal weight:    7.9990
   chunk 72 optimal weight:   20.0000
   chunk 4 optimal weight:   50.0000
   overall best weight:    0.5258

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

Flipped N/Q/H residues before XYZ refinement:
A 288 ASN
B 294 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4614 r_free = 0.4614 target = 0.199983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.157830 restraints weight = 17620.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.152766 restraints weight = 11684.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.154385 restraints weight = 10576.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.4045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7097
moved from start:          0.2256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8637  Z= 0.177
  Angle     :  0.580   9.972  11823  Z= 0.309
  Chirality :  0.037   0.140   1375
  Planarity :  0.004   0.081   1499
  Dihedral  :  3.914  21.569   1239
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.16 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 25.50 %
    Favored  : 70.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.46 (0.25), residues: 1153
  helix:  2.69 (0.17), residues: 875
  sheet:  None (None), residues: 0
  loop : -2.08 (0.35), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 373 
 HIS   0.004   0.001   HIS B 499 
 PHE   0.017   0.001   PHE B 487 
 TYR   0.037   0.001   TYR B 412 
 ARG   0.003   0.000   ARG B 308 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 159
  time to evaluate  : 0.879 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 TYR cc_start: 0.7041 (t80) cc_final: 0.6424 (t80)
REVERT: B  244 PHE cc_start: 0.8075 (t80) cc_final: 0.7180 (t80)
REVERT: B  409 ASP cc_start: 0.6350 (p0) cc_final: 0.5956 (p0)
REVERT: B  495 LEU cc_start: 0.8129 (pp) cc_final: 0.7916 (pp)
  outliers start: 28
  outliers final: 21
  residues processed: 174
  average time/residue: 0.1472
  time to fit residues: 38.1887
Evaluate side-chains
  167 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 146
  time to evaluate  : 0.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  310 ASN
Chi-restraints excluded: chain A residue  336 PHE
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  278 LEU
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  396 LEU
Chi-restraints excluded: chain B residue  474 PHE
Chi-restraints excluded: chain B residue  489 MET
Chi-restraints excluded: chain B residue  492 PHE
Chi-restraints excluded: chain B residue  496 TYR
Chi-restraints excluded: chain B residue  530 LEU
Chi-restraints excluded: chain B residue  616 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 6 optimal weight:    8.9990
   chunk 48 optimal weight:    0.9980
   chunk 91 optimal weight:    0.3980
   chunk 7 optimal weight:   10.0000
   chunk 40 optimal weight:    4.9990
   chunk 66 optimal weight:   40.0000
   chunk 8 optimal weight:   40.0000
   chunk 22 optimal weight:    0.9980
   chunk 105 optimal weight:    0.8980
   chunk 63 optimal weight:   10.0000
   chunk 106 optimal weight:    0.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 479 ASN
B 499 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4601 r_free = 0.4601 target = 0.197975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.158088 restraints weight = 17682.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.152090 restraints weight = 11625.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.153778 restraints weight = 10802.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.4037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7110
moved from start:          0.2445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8637  Z= 0.197
  Angle     :  0.590   9.947  11823  Z= 0.313
  Chirality :  0.038   0.142   1375
  Planarity :  0.004   0.076   1499
  Dihedral  :  3.809  19.115   1239
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.42 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 24.93 %
    Favored  : 70.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.50 (0.25), residues: 1153
  helix:  2.67 (0.17), residues: 880
  sheet:  None (None), residues: 0
  loop : -1.99 (0.35), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 373 
 HIS   0.003   0.001   HIS A 299 
 PHE   0.027   0.001   PHE A 511 
 TYR   0.037   0.001   TYR B 412 
 ARG   0.003   0.000   ARG B 459 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 151
  time to evaluate  : 1.004 
Fit side-chains
   revert: symmetry clash
REVERT: A  479 ASN cc_start: 0.6731 (OUTLIER) cc_final: 0.6484 (t0)
REVERT: B  244 PHE cc_start: 0.8158 (t80) cc_final: 0.7250 (t80)
REVERT: B  266 TRP cc_start: 0.8343 (m100) cc_final: 0.8132 (m100)
REVERT: B  495 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7779 (pp)
  outliers start: 31
  outliers final: 22
  residues processed: 169
  average time/residue: 0.1640
  time to fit residues: 41.1014
Evaluate side-chains
  166 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 142
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  310 ASN
Chi-restraints excluded: chain A residue  336 PHE
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  479 ASN
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  278 LEU
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  396 LEU
Chi-restraints excluded: chain B residue  474 PHE
Chi-restraints excluded: chain B residue  489 MET
Chi-restraints excluded: chain B residue  492 PHE
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  496 TYR
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  530 LEU
Chi-restraints excluded: chain B residue  616 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 62 optimal weight:   80.0000
   chunk 112 optimal weight:    0.8980
   chunk 77 optimal weight:    0.6980
   chunk 41 optimal weight:    0.3980
   chunk 71 optimal weight:    0.8980
   chunk 97 optimal weight:    0.0040
   chunk 18 optimal weight:    0.0470
   chunk 39 optimal weight:    0.5980
   chunk 70 optimal weight:    9.9990
   chunk 8 optimal weight:   20.0000
   chunk 87 optimal weight:    0.6980
   overall best weight:    0.3490

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

Flipped N/Q/H residues before XYZ refinement:
A 479 ASN
B 294 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4615 r_free = 0.4615 target = 0.199445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.158717 restraints weight = 17864.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.153685 restraints weight = 11971.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.155460 restraints weight = 11228.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.4069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7064
moved from start:          0.2549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8637  Z= 0.169
  Angle     :  0.578  10.055  11823  Z= 0.307
  Chirality :  0.037   0.141   1375
  Planarity :  0.004   0.073   1499
  Dihedral  :  3.788  18.373   1239
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.25 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 25.93 %
    Favored  : 69.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.57 (0.26), residues: 1153
  helix:  2.71 (0.17), residues: 881
  sheet:  None (None), residues: 0
  loop : -1.96 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 373 
 HIS   0.003   0.001   HIS A 299 
 PHE   0.025   0.001   PHE A 511 
 TYR   0.038   0.001   TYR B 412 
 ARG   0.002   0.000   ARG A 465 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 150
  time to evaluate  : 0.901 
Fit side-chains
   revert: symmetry clash
REVERT: B  244 PHE cc_start: 0.8107 (t80) cc_final: 0.7169 (t80)
REVERT: B  409 ASP cc_start: 0.6015 (p0) cc_final: 0.5500 (p0)
REVERT: B  495 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7788 (pp)
  outliers start: 29
  outliers final: 23
  residues processed: 166
  average time/residue: 0.1531
  time to fit residues: 38.1704
Evaluate side-chains
  167 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 143
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  310 ASN
Chi-restraints excluded: chain A residue  336 PHE
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  415 CYS
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  278 LEU
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  396 LEU
Chi-restraints excluded: chain B residue  474 PHE
Chi-restraints excluded: chain B residue  492 PHE
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  496 TYR
Chi-restraints excluded: chain B residue  499 HIS
Chi-restraints excluded: chain B residue  530 LEU
Chi-restraints excluded: chain B residue  583 THR
Chi-restraints excluded: chain B residue  616 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 40 optimal weight:    6.9990
   chunk 47 optimal weight:    6.9990
   chunk 100 optimal weight:    4.9990
   chunk 94 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 55 optimal weight:    0.0170
   chunk 12 optimal weight:    5.9990
   chunk 71 optimal weight:    5.9990
   chunk 41 optimal weight:    0.0870
   overall best weight:    0.5598

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4602 r_free = 0.4602 target = 0.198997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.157327 restraints weight = 18045.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.153811 restraints weight = 11311.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.155162 restraints weight = 10039.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.4074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7039
moved from start:          0.2664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8637  Z= 0.171
  Angle     :  0.570  10.067  11823  Z= 0.303
  Chirality :  0.038   0.142   1375
  Planarity :  0.004   0.072   1499
  Dihedral  :  3.713  18.190   1239
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.34 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 26.92 %
    Favored  : 69.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.59 (0.26), residues: 1153
  helix:  2.71 (0.17), residues: 883
  sheet:  None (None), residues: 0
  loop : -1.92 (0.36), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A 373 
 HIS   0.003   0.001   HIS B 441 
 PHE   0.030   0.001   PHE A 511 
 TYR   0.034   0.001   TYR B 412 
 ARG   0.002   0.000   ARG B 459 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 147
  time to evaluate  : 0.901 
Fit side-chains
   revert: symmetry clash
REVERT: A  418 SER cc_start: 0.8709 (m) cc_final: 0.8261 (p)
REVERT: B  244 PHE cc_start: 0.8092 (t80) cc_final: 0.7154 (t80)
REVERT: B  495 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7792 (pp)
  outliers start: 26
  outliers final: 23
  residues processed: 160
  average time/residue: 0.1495
  time to fit residues: 36.1676
Evaluate side-chains
  167 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 143
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  310 ASN
Chi-restraints excluded: chain A residue  336 PHE
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  415 CYS
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  278 LEU
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  396 LEU
Chi-restraints excluded: chain B residue  474 PHE
Chi-restraints excluded: chain B residue  492 PHE
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  499 HIS
Chi-restraints excluded: chain B residue  530 LEU
Chi-restraints excluded: chain B residue  583 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 103 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 77 optimal weight:    0.5980
   chunk 63 optimal weight:    8.9990
   chunk 42 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0270
   chunk 45 optimal weight:    0.9980
   chunk 69 optimal weight:   50.0000
   chunk 35 optimal weight:    0.7980
   chunk 90 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9990
   overall best weight:    0.6438

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4612 r_free = 0.4612 target = 0.198998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.157130 restraints weight = 18067.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.153899 restraints weight = 10537.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.155678 restraints weight = 9584.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.4081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7047
moved from start:          0.2736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8637  Z= 0.180
  Angle     :  0.603  15.433  11823  Z= 0.313
  Chirality :  0.038   0.199   1375
  Planarity :  0.004   0.071   1499
  Dihedral  :  3.700  18.098   1239
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.25 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 27.35 %
    Favored  : 68.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.62 (0.26), residues: 1153
  helix:  2.73 (0.17), residues: 883
  sheet:  None (None), residues: 0
  loop : -1.90 (0.36), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 373 
 HIS   0.004   0.001   HIS A 587 
 PHE   0.016   0.001   PHE B 487 
 TYR   0.032   0.001   TYR B 412 
 ARG   0.002   0.000   ARG B 270 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 145
  time to evaluate  : 0.880 
Fit side-chains
   revert: symmetry clash
REVERT: A  418 SER cc_start: 0.8727 (m) cc_final: 0.8244 (p)
REVERT: B  244 PHE cc_start: 0.8179 (t80) cc_final: 0.7237 (t80)
REVERT: B  495 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7758 (pp)
  outliers start: 26
  outliers final: 22
  residues processed: 157
  average time/residue: 0.1440
  time to fit residues: 34.0142
Evaluate side-chains
  164 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 141
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  310 ASN
Chi-restraints excluded: chain A residue  336 PHE
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  415 CYS
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain B residue  278 LEU
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  396 LEU
Chi-restraints excluded: chain B residue  474 PHE
Chi-restraints excluded: chain B residue  492 PHE
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  496 TYR
Chi-restraints excluded: chain B residue  499 HIS
Chi-restraints excluded: chain B residue  530 LEU
Chi-restraints excluded: chain B residue  583 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 14 optimal weight:    7.9990
   chunk 65 optimal weight:   20.0000
   chunk 101 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 44 optimal weight:    0.8980
   chunk 15 optimal weight:   30.0000
   chunk 97 optimal weight:    9.9990
   chunk 73 optimal weight:    7.9990
   chunk 24 optimal weight:    0.8980
   chunk 7 optimal weight:   20.0000
   chunk 1 optimal weight:   20.0000
   overall best weight:    2.4784

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

Flipped N/Q/H residues before XYZ refinement:
** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4531 r_free = 0.4531 target = 0.191672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.149056 restraints weight = 17748.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.146347 restraints weight = 11616.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.147263 restraints weight = 10606.777|
|-----------------------------------------------------------------------------|
r_work (final): 0.3982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7158
moved from start:          0.3204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   8637  Z= 0.351
  Angle     :  0.706  15.990  11823  Z= 0.373
  Chirality :  0.043   0.209   1375
  Planarity :  0.005   0.073   1499
  Dihedral  :  4.107  21.043   1239
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.51 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 28.35 %
    Favored  : 68.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.14 (0.25), residues: 1153
  helix:  2.35 (0.17), residues: 878
  sheet:  None (None), residues: 0
  loop : -1.84 (0.37), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP A 373 
 HIS   0.007   0.001   HIS B 313 
 PHE   0.024   0.002   PHE A 511 
 TYR   0.036   0.002   TYR B 412 
 ARG   0.005   0.001   ARG B 604 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 137
  time to evaluate  : 1.105 
Fit side-chains
   revert: symmetry clash
REVERT: A  585 LEU cc_start: 0.4582 (mt) cc_final: 0.4342 (tp)
REVERT: B  244 PHE cc_start: 0.8137 (t80) cc_final: 0.7332 (t80)
REVERT: B  368 TYR cc_start: 0.6886 (p90) cc_final: 0.6590 (p90)
REVERT: B  450 ILE cc_start: 0.9125 (tp) cc_final: 0.8908 (tp)
REVERT: B  495 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7982 (pp)
REVERT: B  506 ASP cc_start: 0.6809 (t0) cc_final: 0.6524 (m-30)
  outliers start: 25
  outliers final: 22
  residues processed: 155
  average time/residue: 0.1525
  time to fit residues: 36.2605
Evaluate side-chains
  151 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 128
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  310 ASN
Chi-restraints excluded: chain A residue  336 PHE
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  415 CYS
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  601 VAL
Chi-restraints excluded: chain B residue  278 LEU
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  396 LEU
Chi-restraints excluded: chain B residue  474 PHE
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  496 TYR
Chi-restraints excluded: chain B residue  499 HIS
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  516 VAL
Chi-restraints excluded: chain B residue  530 LEU
Chi-restraints excluded: chain B residue  583 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 48 optimal weight:    0.5980
   chunk 108 optimal weight:    0.9980
   chunk 38 optimal weight:    0.0670
   chunk 76 optimal weight:    0.0770
   chunk 52 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 15 optimal weight:    8.9990
   chunk 55 optimal weight:    3.9990
   chunk 5 optimal weight:   50.0000
   chunk 19 optimal weight:    1.9990
   chunk 57 optimal weight:    0.7980
   overall best weight:    0.4476

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4601 r_free = 0.4601 target = 0.198204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.155658 restraints weight = 17736.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.152586 restraints weight = 10382.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.154146 restraints weight = 9283.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.4052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7091
moved from start:          0.3207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8637  Z= 0.184
  Angle     :  0.633  16.227  11823  Z= 0.329
  Chirality :  0.039   0.223   1375
  Planarity :  0.004   0.070   1499
  Dihedral  :  3.838  17.590   1239
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.90 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 28.92 %
    Favored  : 67.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.45 (0.25), residues: 1153
  helix:  2.59 (0.17), residues: 881
  sheet:  None (None), residues: 0
  loop : -1.86 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A 373 
 HIS   0.004   0.001   HIS A 587 
 PHE   0.015   0.001   PHE B 487 
 TYR   0.037   0.001   TYR B 412 
 ARG   0.003   0.000   ARG A 465 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2857.30 seconds
wall clock time: 50 minutes 32.94 seconds (3032.94 seconds total)