Starting phenix.real_space_refine
on Wed Jan 15 13:30:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yfw_39231/01_2025/8yfw_39231.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yfw_39231/01_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_39231/01_2025/8yfw_39231.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yfw_39231/01_2025/8yfw_39231.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yfw_39231/01_2025/8yfw_39231.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yfw_39231/01_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-5571/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: 5.21, per 1000 atoms: 0.62
  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: 2.46
  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: 0.64
  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: 2.30

  Time building geometry restraints manager: 2.75 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:             1.400
  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:             0.000
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     21.370
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.360
-------------------------------------------------------------------------------
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  : 0.720 
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: 0.1537
  time to fit residues: 33.9012
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  : 0.856 
-------------------------------------------------------------------------------
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 = 18176.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.157702 restraints weight = 13997.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.157286 restraints weight = 11391.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.4082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6992
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  : 0.868 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 TYR cc_start: 0.7237 (t80) cc_final: 0.6861 (t80)
  outliers start: 25
  outliers final: 11
  residues processed: 169
  average time/residue: 0.1666
  time to fit residues: 41.3715
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  : 0.919 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 62 optimal weight:   80.0000
   chunk 27 optimal weight:    1.9990
   chunk 65 optimal weight:    8.9990
   chunk 71 optimal weight:    0.0570
   chunk 91 optimal weight:    2.9990
   chunk 76 optimal weight:   20.0000
   chunk 87 optimal weight:    0.0030
   chunk 55 optimal weight:    1.9990
   chunk 3 optimal weight:   40.0000
   chunk 38 optimal weight:    4.9990
   overall best weight:    0.9912

-------------------------------------------------------------------------------
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 = 0.4609 r_free = 0.4609 target = 0.199528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.157273 restraints weight = 18339.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.154410 restraints weight = 11475.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.156033 restraints weight = 9785.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.4080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7003
moved from start:          0.1392

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= 0.203
  Angle     :  0.591   9.969  11823  Z= 0.316
  Chirality :  0.039   0.140   1375
  Planarity :  0.004   0.093   1499
  Dihedral  :  3.890  23.864   1239
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.16 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 20.94 %
    Favored  : 74.79 %
  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:  2.38 (0.25), residues: 1153
  helix:  2.63 (0.17), residues: 875
  sheet:  None (None), residues: 0
  loop : -2.13 (0.35), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 373 
 HIS   0.004   0.001   HIS B 313 
 PHE   0.023   0.001   PHE B 335 
 TYR   0.033   0.002   TYR B 412 
 ARG   0.004   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
  179 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 149
  time to evaluate  : 0.895 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 TYR cc_start: 0.6929 (t80) cc_final: 0.6346 (t80)
  outliers start: 30
  outliers final: 18
  residues processed: 166
  average time/residue: 0.1682
  time to fit residues: 41.2761
Evaluate side-chains
  155 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 137
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
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  288 ASN
Chi-restraints excluded: chain A residue  301 LEU
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  576 GLN
Chi-restraints excluded: chain B residue  326 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  616 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 13 optimal weight:   30.0000
   chunk 112 optimal weight:    0.0170
   chunk 46 optimal weight:    6.9990
   chunk 41 optimal weight:    2.9990
   chunk 70 optimal weight:   20.0000
   chunk 71 optimal weight:    0.9990
   chunk 114 optimal weight:    2.9990
   chunk 82 optimal weight:    0.6980
   chunk 80 optimal weight:    0.6980
   chunk 88 optimal weight:    3.9990
   chunk 108 optimal weight:    8.9990
   overall best weight:    1.0822

-------------------------------------------------------------------------------
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 = 0.4606 r_free = 0.4606 target = 0.199570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.156585 restraints weight = 18276.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.153815 restraints weight = 11790.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.154545 restraints weight = 11487.621|
|-----------------------------------------------------------------------------|
r_work (final): 0.4063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7050
moved from start:          0.1756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8637  Z= 0.212
  Angle     :  0.581   9.959  11823  Z= 0.312
  Chirality :  0.039   0.157   1375
  Planarity :  0.004   0.084   1499
  Dihedral  :  3.805  19.445   1239
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.25 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 23.36 %
    Favored  : 72.79 %
  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:  2.72 (0.17), residues: 869
  sheet:  None (None), residues: 0
  loop : -2.12 (0.35), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 528 
 HIS   0.004   0.001   HIS A 299 
 PHE   0.020   0.001   PHE B 487 
 TYR   0.040   0.002   TYR B 412 
 ARG   0.003   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
  178 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 151
  time to evaluate  : 0.975 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 TYR cc_start: 0.6988 (t80) cc_final: 0.6397 (t80)
REVERT: B  244 PHE cc_start: 0.7995 (t80) cc_final: 0.7310 (t80)
REVERT: B  364 LYS cc_start: 0.7587 (tttt) cc_final: 0.7246 (mmpt)
  outliers start: 27
  outliers final: 20
  residues processed: 164
  average time/residue: 0.1577
  time to fit residues: 38.5123
Evaluate side-chains
  159 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 139
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
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  288 ASN
Chi-restraints excluded: chain A residue  294 GLN
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  576 GLN
Chi-restraints excluded: chain B residue  239 LEU
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  474 PHE
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  616 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 102 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 73 optimal weight:    7.9990
   chunk 18 optimal weight:   30.0000
   chunk 50 optimal weight:    0.0980
   chunk 43 optimal weight:    3.9990
   chunk 109 optimal weight:    0.0070
   chunk 59 optimal weight:    8.9990
   chunk 72 optimal weight:   10.0000
   chunk 4 optimal weight:   50.0000
   overall best weight:    0.5000

-------------------------------------------------------------------------------
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 = 0.4624 r_free = 0.4624 target = 0.201005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.158632 restraints weight = 17817.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.155407 restraints weight = 11457.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.156639 restraints weight = 11251.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.4091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7012
moved from start:          0.2003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8637  Z= 0.165
  Angle     :  0.564  10.029  11823  Z= 0.300
  Chirality :  0.038   0.149   1375
  Planarity :  0.004   0.078   1499
  Dihedral  :  3.743  18.205   1239
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.08 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 24.07 %
    Favored  : 71.65 %
  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:  2.61 (0.25), residues: 1153
  helix:  2.82 (0.17), residues: 871
  sheet:  None (None), residues: 0
  loop : -2.05 (0.35), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 292 
 HIS   0.003   0.001   HIS B 441 
 PHE   0.024   0.001   PHE A 511 
 TYR   0.038   0.001   TYR B 412 
 ARG   0.004   0.000   ARG B 448 

*********************** 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
  183 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 153
  time to evaluate  : 0.883 
Fit side-chains
   revert: symmetry clash
REVERT: B  244 PHE cc_start: 0.7965 (t80) cc_final: 0.7202 (t80)
REVERT: B  364 LYS cc_start: 0.7495 (tttt) cc_final: 0.7151 (mmpt)
REVERT: B  409 ASP cc_start: 0.6259 (p0) cc_final: 0.5900 (p0)
  outliers start: 30
  outliers final: 22
  residues processed: 168
  average time/residue: 0.1654
  time to fit residues: 41.2678
Evaluate side-chains
  161 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 139
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  288 ASN
Chi-restraints excluded: chain A residue  301 LEU
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  478 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  408 MET
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  499 HIS
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 6 optimal weight:    8.9990
   chunk 48 optimal weight:    2.9990
   chunk 91 optimal weight:    0.8980
   chunk 7 optimal weight:    8.9990
   chunk 40 optimal weight:   10.0000
   chunk 66 optimal weight:   30.0000
   chunk 8 optimal weight:   40.0000
   chunk 22 optimal weight:    0.7980
   chunk 105 optimal weight:    0.9990
   chunk 63 optimal weight:    8.9990
   chunk 106 optimal weight:    1.9990
   overall best weight:    1.5386

-------------------------------------------------------------------------------
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 = 0.198855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.156354 restraints weight = 17752.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.151959 restraints weight = 11408.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.153886 restraints weight = 10349.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.4055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7081
moved from start:          0.2300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8637  Z= 0.243
  Angle     :  0.603  10.076  11823  Z= 0.323
  Chirality :  0.040   0.173   1375
  Planarity :  0.004   0.074   1499
  Dihedral  :  3.809  19.607   1239
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.25 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 24.07 %
    Favored  : 71.08 %
  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:  2.48 (0.25), residues: 1153
  helix:  2.68 (0.17), residues: 873
  sheet:  None (None), residues: 0
  loop : -1.97 (0.35), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 266 
 HIS   0.004   0.001   HIS B 313 
 PHE   0.059   0.002   PHE B 416 
 TYR   0.039   0.002   TYR B 412 
 ARG   0.005   0.000   ARG B 270 

*********************** 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
  179 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 145
  time to evaluate  : 1.088 
Fit side-chains
   revert: symmetry clash
REVERT: B  244 PHE cc_start: 0.8123 (t80) cc_final: 0.7290 (t80)
REVERT: B  364 LYS cc_start: 0.7688 (tttt) cc_final: 0.7363 (mmpt)
  outliers start: 34
  outliers final: 26
  residues processed: 166
  average time/residue: 0.1601
  time to fit residues: 39.5078
Evaluate side-chains
  158 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 132
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
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  241 CYS
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  288 ASN
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 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  496 TYR
Chi-restraints excluded: chain B residue  499 HIS
Chi-restraints excluded: chain B residue  509 VAL
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 62 optimal weight:   80.0000
   chunk 112 optimal weight:    1.9990
   chunk 77 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9980
   chunk 71 optimal weight:    0.0670
   chunk 97 optimal weight:    0.5980
   chunk 18 optimal weight:   40.0000
   chunk 39 optimal weight:    0.1980
   chunk 70 optimal weight:   10.0000
   chunk 8 optimal weight:   20.0000
   chunk 87 optimal weight:    0.0070
   overall best weight:    0.3336

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4631 r_free = 0.4631 target = 0.201630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.160118 restraints weight = 17807.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.155847 restraints weight = 11205.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.157679 restraints weight = 10160.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.4108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6998
moved from start:          0.2442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8637  Z= 0.160
  Angle     :  0.575   9.992  11823  Z= 0.302
  Chirality :  0.038   0.140   1375
  Planarity :  0.003   0.070   1499
  Dihedral  :  3.677  17.841   1239
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.08 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 24.50 %
    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:  2.66 (0.25), residues: 1153
  helix:  2.80 (0.17), residues: 875
  sheet:  None (None), residues: 0
  loop : -1.90 (0.36), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 292 
 HIS   0.003   0.001   HIS A 299 
 PHE   0.029   0.001   PHE A 511 
 TYR   0.036   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: 28
    poor density    : 151
  time to evaluate  : 0.894 
Fit side-chains
   revert: symmetry clash
REVERT: B  244 PHE cc_start: 0.8044 (t80) cc_final: 0.7207 (t80)
  outliers start: 28
  outliers final: 23
  residues processed: 164
  average time/residue: 0.1628
  time to fit residues: 39.5086
Evaluate side-chains
  161 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 138
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
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  287 ILE
Chi-restraints excluded: chain A residue  288 ASN
Chi-restraints excluded: chain A residue  310 ASN
Chi-restraints excluded: chain A residue  336 PHE
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  458 LEU
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  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:    5.9990
   chunk 47 optimal weight:    6.9990
   chunk 100 optimal weight:    4.9990
   chunk 94 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   chunk 12 optimal weight:   20.0000
   chunk 71 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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 = 0.4607 r_free = 0.4607 target = 0.199229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.157384 restraints weight = 17845.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.153132 restraints weight = 10960.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.154601 restraints weight = 10030.482|
|-----------------------------------------------------------------------------|
r_work (final): 0.4070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7049
moved from start:          0.2612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8637  Z= 0.216
  Angle     :  0.589  10.054  11823  Z= 0.316
  Chirality :  0.039   0.141   1375
  Planarity :  0.004   0.071   1499
  Dihedral  :  3.709  18.566   1239
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.16 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 26.07 %
    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:  2.60 (0.25), residues: 1153
  helix:  2.75 (0.17), residues: 873
  sheet:  None (None), residues: 0
  loop : -1.86 (0.36), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 292 
 HIS   0.004   0.001   HIS B 313 
 PHE   0.059   0.002   PHE B 416 
 TYR   0.034   0.002   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
  169 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 141
  time to evaluate  : 0.924 
Fit side-chains
   revert: symmetry clash
REVERT: A  294 GLN cc_start: 0.6621 (tm-30) cc_final: 0.6258 (tm-30)
REVERT: B  244 PHE cc_start: 0.8106 (t80) cc_final: 0.7258 (t80)
  outliers start: 28
  outliers final: 23
  residues processed: 155
  average time/residue: 0.1559
  time to fit residues: 36.0584
Evaluate side-chains
  160 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 137
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
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  288 ASN
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  310 ASN
Chi-restraints excluded: chain A residue  336 PHE
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  326 LEU
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  351 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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 103 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 77 optimal weight:    0.7980
   chunk 63 optimal weight:   10.0000
   chunk 42 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0770
   chunk 45 optimal weight:    0.9990
   chunk 69 optimal weight:   50.0000
   chunk 35 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9980
   chunk 99 optimal weight:    0.3980
   overall best weight:    0.5338

-------------------------------------------------------------------------------
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 = 0.4625 r_free = 0.4625 target = 0.200962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.158605 restraints weight = 17839.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.154755 restraints weight = 10905.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.156482 restraints weight = 10170.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.4078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7053
moved from start:          0.2739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8637  Z= 0.171
  Angle     :  0.589  10.068  11823  Z= 0.306
  Chirality :  0.038   0.147   1375
  Planarity :  0.003   0.069   1499
  Dihedral  :  3.644  17.416   1239
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.90 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 26.07 %
    Favored  : 70.37 %
  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:  2.72 (0.25), residues: 1153
  helix:  2.84 (0.17), residues: 875
  sheet:  None (None), residues: 0
  loop : -1.86 (0.36), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 292 
 HIS   0.003   0.001   HIS A 299 
 PHE   0.030   0.001   PHE A 511 
 TYR   0.031   0.001   TYR B 412 
 ARG   0.002   0.000   ARG B 472 

*********************** 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
  169 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 144
  time to evaluate  : 0.944 
Fit side-chains
   revert: symmetry clash
REVERT: A  294 GLN cc_start: 0.6513 (tm-30) cc_final: 0.6195 (tm-30)
REVERT: B  244 PHE cc_start: 0.8121 (t80) cc_final: 0.7211 (t80)
  outliers start: 25
  outliers final: 23
  residues processed: 158
  average time/residue: 0.1484
  time to fit residues: 35.3593
Evaluate side-chains
  157 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 134
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
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  288 ASN
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 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  351 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  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:   20.0000
   chunk 65 optimal weight:    9.9990
   chunk 101 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 15 optimal weight:   30.0000
   chunk 97 optimal weight:    0.0270
   chunk 73 optimal weight:    9.9990
   chunk 24 optimal weight:    0.6980
   chunk 7 optimal weight:   10.0000
   chunk 1 optimal weight:    8.9990
   overall best weight:    1.2842

-------------------------------------------------------------------------------
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 = 0.198782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.156628 restraints weight = 17658.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.152608 restraints weight = 11220.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.154027 restraints weight = 11538.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.4059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7078
moved from start:          0.2885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8637  Z= 0.230
  Angle     :  0.630  15.316  11823  Z= 0.328
  Chirality :  0.040   0.198   1375
  Planarity :  0.004   0.070   1499
  Dihedral  :  3.726  18.675   1239
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.25 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 26.78 %
    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:  2.62 (0.25), residues: 1153
  helix:  2.74 (0.17), residues: 876
  sheet:  None (None), residues: 0
  loop : -1.81 (0.36), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 292 
 HIS   0.004   0.001   HIS B 313 
 PHE   0.051   0.001   PHE B 416 
 TYR   0.033   0.001   TYR B 412 
 ARG   0.004   0.000   ARG B 448 

********************** 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
  157 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 134
  time to evaluate  : 0.895 
Fit side-chains
   revert: symmetry clash
REVERT: A  294 GLN cc_start: 0.6552 (tm-30) cc_final: 0.6260 (tm-30)
REVERT: B  244 PHE cc_start: 0.8162 (t80) cc_final: 0.7276 (t80)
  outliers start: 23
  outliers final: 22
  residues processed: 146
  average time/residue: 0.1440
  time to fit residues: 32.3716
Evaluate side-chains
  154 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 132
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
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  288 ASN
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 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  351 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  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 48 optimal weight:    0.7980
   chunk 108 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 76 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 15 optimal weight:   50.0000
   chunk 55 optimal weight:    0.8980
   chunk 5 optimal weight:   50.0000
   chunk 19 optimal weight:    0.2980
   chunk 57 optimal weight:    0.7980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.4615 r_free = 0.4615 target = 0.199990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.157252 restraints weight = 17885.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.153174 restraints weight = 10887.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.155086 restraints weight = 10155.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.4060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7090
moved from start:          0.2994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8637  Z= 0.185
  Angle     :  0.624  15.972  11823  Z= 0.321
  Chirality :  0.039   0.157   1375
  Planarity :  0.004   0.068   1499
  Dihedral  :  3.677  17.793   1239
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.64 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 27.64 %
    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:  2.71 (0.25), residues: 1153
  helix:  2.81 (0.17), residues: 875
  sheet:  None (None), residues: 0
  loop : -1.78 (0.36), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 292 
 HIS   0.004   0.001   HIS A 587 
 PHE   0.031   0.001   PHE A 511 
 TYR   0.039   0.001   TYR B 412 
 ARG   0.002   0.000   ARG A 465 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2652.41 seconds
wall clock time: 48 minutes 7.18 seconds (2887.18 seconds total)