Starting phenix.real_space_refine
on Wed Sep 17 11:37:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yfw_39231/09_2025/8yfw_39231.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yfw_39231/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yfw_39231/09_2025/8yfw_39231.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yfw_39231/09_2025/8yfw_39231.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yfw_39231/09_2025/8yfw_39231.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yfw_39231/09_2025/8yfw_39231.map"
  }
  resolution = 3.65
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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, 'TYR:plan': 7, 'GLU:plan': 20, 'PHE:plan': 12, 'ASP:plan': 10, 'ARG:plan': 11, 'ASN:plan1': 8, 'HIS:plan': 4, 'TRP:plan': 1}
          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: {'ASP:plan': 10, 'TYR:plan': 6, 'GLN:plan1': 12, 'GLU:plan': 19, 'ARG:plan': 11, 'PHE:plan': 11, 'ASN:plan1': 8, 'HIS:plan': 4, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 370
  Time building chain proxies: 2.44, per 1000 atoms: 0.29
  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: 0.93
  Conformation dependent library (CDL) restraints added in 365.4 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.24
  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: 1.27

  Time building geometry restraints manager: 1.18 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:             1.110
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.840
  Find NCS groups from input model:        0.140
  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:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.640
-------------------------------------------------------------------------------
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   8639  Z= 0.157
  Angle     :  0.747  19.928  11827  Z= 0.413
  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 : 13.10
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.007   0.001   ARG B 270 
 TYR   0.033   0.002   TYR B 412 
 PHE   0.028   0.002   PHE B 357 
 TRP   0.037   0.002   TRP A 373 
 HIS   0.005   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 8637)
  covalent geometry    : angle       0.73731 (11823)
  SS BOND              : bond        0.00141 (    2)
  SS BOND              : angle       6.49003 (    4)
  hydrogen bonds       : bond        0.12957 (  667)
  hydrogen bonds       : angle       5.64915 ( 2001)

*********************** 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  : 0.320 
Fit side-chains
REVERT: B  506 ASP cc_start: 0.6490 (t0) cc_final: 0.6279 (t0)
  outliers start: 2
  outliers final: 1
  residues processed: 148
  average time/residue: 0.0704
  time to fit residues: 15.7888
Evaluate side-chains
  144 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 143
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  241 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    0.9980
   chunk 113 optimal weight:    0.6980
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:   50.0000
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:   80.0000
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    0.0670
   overall best weight:    0.6518

-------------------------------------------------------------------------------
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 = 0.4634 r_free = 0.4634 target = 0.202837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.158383 restraints weight = 18391.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.157526 restraints weight = 14320.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.157343 restraints weight = 10976.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.158210 restraints weight = 9413.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.158565 restraints weight = 8305.553|
|-----------------------------------------------------------------------------|
r_work (final): 0.4113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6967
moved from start:          0.0929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8639  Z= 0.139
  Angle     :  0.604   9.828  11827  Z= 0.325
  Chirality :  0.039   0.161   1375
  Planarity :  0.005   0.122   1499
  Dihedral  :  4.046  27.117   1240
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.08 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 23.22 %
    Favored  : 73.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.20 (0.25), residues: 1153
  helix:  2.52 (0.17), residues: 867
  sheet:  None (None), residues: 0
  loop : -2.12 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 465 
 TYR   0.026   0.001   TYR B 412 
 PHE   0.026   0.002   PHE B 335 
 TRP   0.017   0.002   TRP A 373 
 HIS   0.004   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 8637)
  covalent geometry    : angle       0.60046 (11823)
  SS BOND              : bond        0.00545 (    2)
  SS BOND              : angle       3.63979 (    4)
  hydrogen bonds       : bond        0.04549 (  667)
  hydrogen bonds       : angle       4.02755 ( 2001)

*********************** 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  : 0.318 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 TYR cc_start: 0.7261 (t80) cc_final: 0.6843 (t80)
  outliers start: 25
  outliers final: 12
  residues processed: 169
  average time/residue: 0.0772
  time to fit residues: 19.4360
Evaluate side-chains
  155 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 143
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
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 A residue  576 GLN
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 84 optimal weight:    0.0020
   chunk 39 optimal weight:    0.0980
   chunk 54 optimal weight:   10.0000
   chunk 49 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 106 optimal weight:    0.7980
   chunk 41 optimal weight:    3.9990
   chunk 61 optimal weight:   50.0000
   chunk 7 optimal weight:   30.0000
   chunk 97 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   overall best weight:    1.1792

-------------------------------------------------------------------------------
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 = 0.4605 r_free = 0.4605 target = 0.199862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.156674 restraints weight = 18152.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.153592 restraints weight = 12324.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.154504 restraints weight = 11201.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.154767 restraints weight = 9226.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.154838 restraints weight = 8617.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.4058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7057
moved from start:          0.1372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8639  Z= 0.147
  Angle     :  0.594  10.011  11827  Z= 0.318
  Chirality :  0.039   0.142   1375
  Planarity :  0.004   0.092   1499
  Dihedral  :  3.919  24.411   1239
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.42 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 21.79 %
    Favored  : 73.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.35 (0.25), residues: 1153
  helix:  2.60 (0.17), residues: 876
  sheet:  None (None), residues: 0
  loop : -2.11 (0.35), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 466 
 TYR   0.033   0.002   TYR B 412 
 PHE   0.041   0.002   PHE B 416 
 TRP   0.021   0.002   TRP A 373 
 HIS   0.005   0.001   HIS B 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 8637)
  covalent geometry    : angle       0.59217 (11823)
  SS BOND              : bond        0.00791 (    2)
  SS BOND              : angle       2.34795 (    4)
  hydrogen bonds       : bond        0.04328 (  667)
  hydrogen bonds       : angle       3.73900 ( 2001)

*********************** 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
  180 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 150
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  290 TYR cc_start: 0.6996 (t80) cc_final: 0.6477 (t80)
REVERT: B  244 PHE cc_start: 0.8026 (t80) cc_final: 0.7547 (t80)
REVERT: B  411 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7523 (tm-30)
  outliers start: 30
  outliers final: 19
  residues processed: 170
  average time/residue: 0.0741
  time to fit residues: 18.8091
Evaluate side-chains
  152 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 133
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
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  458 LEU
Chi-restraints excluded: chain B residue  284 LEU
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 20 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 90 optimal weight:    0.0670
   chunk 77 optimal weight:    0.5980
   chunk 47 optimal weight:    1.9990
   chunk 74 optimal weight:    8.9990
   chunk 76 optimal weight:   10.0000
   chunk 89 optimal weight:    0.8980
   chunk 0 optimal weight:   30.0000
   chunk 55 optimal weight:    5.9990
   chunk 58 optimal weight:   50.0000
   overall best weight:    1.3122

-------------------------------------------------------------------------------
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 = 0.4597 r_free = 0.4597 target = 0.199102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.157227 restraints weight = 18425.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.154822 restraints weight = 12528.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.155494 restraints weight = 10409.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.155844 restraints weight = 8203.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.155866 restraints weight = 7747.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.4090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7007
moved from start:          0.1832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8639  Z= 0.152
  Angle     :  0.587   9.845  11827  Z= 0.316
  Chirality :  0.039   0.149   1375
  Planarity :  0.004   0.083   1499
  Dihedral  :  3.906  22.396   1239
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.16 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 22.93 %
    Favored  : 72.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.38 (0.25), residues: 1153
  helix:  2.66 (0.17), residues: 869
  sheet:  None (None), residues: 0
  loop : -2.13 (0.34), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 270 
 TYR   0.031   0.002   TYR B 412 
 PHE   0.020   0.001   PHE B 487 
 TRP   0.019   0.002   TRP A 373 
 HIS   0.004   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 8637)
  covalent geometry    : angle       0.58591 (11823)
  SS BOND              : bond        0.00656 (    2)
  SS BOND              : angle       2.09576 (    4)
  hydrogen bonds       : bond        0.04261 (  667)
  hydrogen bonds       : angle       3.64079 ( 2001)

*********************** 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
  190 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 155
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  290 TYR cc_start: 0.7072 (t80) cc_final: 0.6423 (t80)
REVERT: B  244 PHE cc_start: 0.7993 (t80) cc_final: 0.7273 (t80)
REVERT: B  364 LYS cc_start: 0.7610 (tttt) cc_final: 0.7330 (mmpt)
REVERT: B  412 TYR cc_start: 0.4107 (m-80) cc_final: 0.3878 (m-80)
  outliers start: 35
  outliers final: 27
  residues processed: 175
  average time/residue: 0.0692
  time to fit residues: 17.8957
Evaluate side-chains
  169 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 142
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
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  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  478 VAL
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  284 LEU
Chi-restraints excluded: chain B residue  326 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  591 ILE
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 113 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0050
   chunk 91 optimal weight:    0.8980
   chunk 18 optimal weight:   20.0000
   chunk 89 optimal weight:    2.9990
   chunk 1 optimal weight:    7.9990
   chunk 98 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 65 optimal weight:   50.0000
   chunk 43 optimal weight:    5.9990
   chunk 40 optimal weight:    0.3980
   overall best weight:    0.6394

-------------------------------------------------------------------------------
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 = 0.4634 r_free = 0.4634 target = 0.201701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.158947 restraints weight = 18090.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.154685 restraints weight = 11232.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.156585 restraints weight = 10310.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.156705 restraints weight = 8074.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.156667 restraints weight = 7819.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.4079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7056
moved from start:          0.2049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8639  Z= 0.123
  Angle     :  0.567   9.969  11827  Z= 0.302
  Chirality :  0.038   0.148   1375
  Planarity :  0.004   0.078   1499
  Dihedral  :  3.804  20.642   1239
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.90 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 24.79 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.60 (0.25), residues: 1153
  helix:  2.80 (0.17), residues: 872
  sheet:  None (None), residues: 0
  loop : -2.02 (0.35), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 270 
 TYR   0.038   0.001   TYR B 412 
 PHE   0.025   0.001   PHE A 511 
 TRP   0.021   0.001   TRP A 373 
 HIS   0.003   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 8637)
  covalent geometry    : angle       0.56562 (11823)
  SS BOND              : bond        0.00672 (    2)
  SS BOND              : angle       2.26239 (    4)
  hydrogen bonds       : bond        0.03913 (  667)
  hydrogen bonds       : angle       3.49474 ( 2001)

*********************** 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
  186 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 157
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
REVERT: A  479 ASN cc_start: 0.6501 (OUTLIER) cc_final: 0.6227 (t0)
REVERT: B  244 PHE cc_start: 0.8000 (t80) cc_final: 0.7193 (t80)
REVERT: B  364 LYS cc_start: 0.7613 (tttt) cc_final: 0.7336 (mmpt)
REVERT: B  412 TYR cc_start: 0.4218 (m-80) cc_final: 0.3811 (m-80)
  outliers start: 29
  outliers final: 22
  residues processed: 173
  average time/residue: 0.0658
  time to fit residues: 17.0843
Evaluate side-chains
  166 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 143
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
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  478 VAL
Chi-restraints excluded: chain A residue  479 ASN
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  284 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  616 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 87 optimal weight:    6.9990
   chunk 69 optimal weight:   50.0000
   chunk 31 optimal weight:    0.7980
   chunk 99 optimal weight:    1.9990
   chunk 112 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 44 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9980
   chunk 43 optimal weight:    4.9990
   chunk 84 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.201137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.158987 restraints weight = 17769.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.154746 restraints weight = 11001.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.156681 restraints weight = 10083.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.156888 restraints weight = 7681.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.156933 restraints weight = 7316.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.4090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7026
moved from start:          0.2179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8639  Z= 0.131
  Angle     :  0.585  10.064  11827  Z= 0.309
  Chirality :  0.038   0.231   1375
  Planarity :  0.004   0.074   1499
  Dihedral  :  3.766  18.817   1239
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.16 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 24.07 %
    Favored  : 71.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.57 (0.25), residues: 1153
  helix:  2.77 (0.17), residues: 872
  sheet:  None (None), residues: 0
  loop : -2.00 (0.35), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 448 
 TYR   0.029   0.001   TYR B 412 
 PHE   0.037   0.001   PHE B 416 
 TRP   0.022   0.002   TRP A 373 
 HIS   0.003   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 8637)
  covalent geometry    : angle       0.58121 (11823)
  SS BOND              : bond        0.02007 (    2)
  SS BOND              : angle       3.45088 (    4)
  hydrogen bonds       : bond        0.03863 (  667)
  hydrogen bonds       : angle       3.51341 ( 2001)

*********************** 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
  184 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 151
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
REVERT: B  244 PHE cc_start: 0.8054 (t80) cc_final: 0.7210 (t80)
REVERT: B  364 LYS cc_start: 0.7662 (tttt) cc_final: 0.7391 (mmpt)
  outliers start: 33
  outliers final: 27
  residues processed: 170
  average time/residue: 0.0699
  time to fit residues: 17.8261
Evaluate side-chains
  171 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 144
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
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  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 B residue  239 LEU
Chi-restraints excluded: chain B residue  278 LEU
Chi-restraints excluded: chain B residue  284 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  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 38 optimal weight:    0.0570
   chunk 23 optimal weight:    0.6980
   chunk 17 optimal weight:   40.0000
   chunk 51 optimal weight:    0.0670
   chunk 108 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 26 optimal weight:    6.9990
   chunk 61 optimal weight:   50.0000
   chunk 54 optimal weight:   10.0000
   chunk 18 optimal weight:   30.0000
   chunk 88 optimal weight:    0.0170
   overall best weight:    0.9676

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4614 r_free = 0.4614 target = 0.199907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.158210 restraints weight = 17978.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.153830 restraints weight = 11278.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.155735 restraints weight = 10027.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.155952 restraints weight = 7717.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.155967 restraints weight = 7312.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.4087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7033
moved from start:          0.2381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8639  Z= 0.132
  Angle     :  0.594  10.005  11827  Z= 0.312
  Chirality :  0.038   0.191   1375
  Planarity :  0.004   0.071   1499
  Dihedral  :  3.716  18.819   1239
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.16 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 23.93 %
    Favored  : 71.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.57 (0.25), residues: 1153
  helix:  2.74 (0.17), residues: 875
  sheet:  None (None), residues: 0
  loop : -1.92 (0.36), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 270 
 TYR   0.040   0.002   TYR B 412 
 PHE   0.028   0.001   PHE A 511 
 TRP   0.025   0.002   TRP A 373 
 HIS   0.003   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 8637)
  covalent geometry    : angle       0.59267 (11823)
  SS BOND              : bond        0.01344 (    2)
  SS BOND              : angle       2.16366 (    4)
  hydrogen bonds       : bond        0.03878 (  667)
  hydrogen bonds       : angle       3.49776 ( 2001)

*********************** 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
  175 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 142
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
REVERT: B  244 PHE cc_start: 0.8108 (t80) cc_final: 0.7231 (t80)
  outliers start: 33
  outliers final: 26
  residues processed: 160
  average time/residue: 0.0691
  time to fit residues: 16.7906
Evaluate side-chains
  163 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 137
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
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  284 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  408 MET
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 68 optimal weight:   50.0000
   chunk 54 optimal weight:   20.0000
   chunk 33 optimal weight:    2.9990
   chunk 14 optimal weight:    9.9990
   chunk 100 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   chunk 73 optimal weight:    8.9990
   chunk 95 optimal weight:    0.9990
   chunk 102 optimal weight:    0.8980
   chunk 108 optimal weight:    4.9990
   chunk 24 optimal weight:    0.7980
   overall best weight:    1.5386

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4588 r_free = 0.4588 target = 0.197356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.155060 restraints weight = 17674.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.150735 restraints weight = 11143.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.152529 restraints weight = 10283.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.152772 restraints weight = 7934.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.152806 restraints weight = 7570.334|
|-----------------------------------------------------------------------------|
r_work (final): 0.4042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7107
moved from start:          0.2704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8639  Z= 0.163
  Angle     :  0.621   9.937  11827  Z= 0.331
  Chirality :  0.039   0.170   1375
  Planarity :  0.004   0.071   1499
  Dihedral  :  3.813  19.831   1239
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.42 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 25.50 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.47 (0.25), residues: 1153
  helix:  2.64 (0.17), residues: 873
  sheet:  None (None), residues: 0
  loop : -1.85 (0.36), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 459 
 TYR   0.027   0.002   TYR B 412 
 PHE   0.017   0.002   PHE A 546 
 TRP   0.024   0.002   TRP A 373 
 HIS   0.005   0.001   HIS B 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 8637)
  covalent geometry    : angle       0.62047 (11823)
  SS BOND              : bond        0.01006 (    2)
  SS BOND              : angle       1.86314 (    4)
  hydrogen bonds       : bond        0.04359 (  667)
  hydrogen bonds       : angle       3.60047 ( 2001)

*********************** 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
  174 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 145
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
REVERT: A  294 GLN cc_start: 0.6594 (tm-30) cc_final: 0.6206 (tm-30)
REVERT: B  244 PHE cc_start: 0.8113 (t80) cc_final: 0.7194 (t80)
REVERT: B  355 MET cc_start: 0.7990 (mmp) cc_final: 0.7539 (mtp)
REVERT: B  409 ASP cc_start: 0.6322 (p0) cc_final: 0.6058 (p0)
REVERT: B  450 ILE cc_start: 0.9096 (tp) cc_final: 0.8891 (tp)
  outliers start: 29
  outliers final: 27
  residues processed: 163
  average time/residue: 0.0654
  time to fit residues: 16.5526
Evaluate side-chains
  168 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 141
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
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 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  284 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  408 MET
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  530 LEU
Chi-restraints excluded: chain B residue  583 THR
Chi-restraints excluded: chain B residue  616 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 36 optimal weight:    0.7980
   chunk 97 optimal weight:    1.9990
   chunk 104 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 72 optimal weight:   20.0000
   chunk 42 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 81 optimal weight:    0.7980
   chunk 15 optimal weight:    5.9990
   chunk 3 optimal weight:   40.0000
   chunk 9 optimal weight:   30.0000
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
B 294 GLN
B 499 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4584 r_free = 0.4584 target = 0.196698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.154451 restraints weight = 17610.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.150179 restraints weight = 11105.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.151521 restraints weight = 11592.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.151818 restraints weight = 8598.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.152115 restraints weight = 7809.953|
|-----------------------------------------------------------------------------|
r_work (final): 0.4035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7120
moved from start:          0.2899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8639  Z= 0.163
  Angle     :  0.628  10.196  11827  Z= 0.331
  Chirality :  0.040   0.169   1375
  Planarity :  0.004   0.069   1499
  Dihedral  :  3.823  19.039   1239
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.16 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 26.21 %
    Favored  : 69.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.45 (0.25), residues: 1153
  helix:  2.62 (0.17), residues: 873
  sheet:  None (None), residues: 0
  loop : -1.83 (0.36), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 459 
 TYR   0.030   0.002   TYR B 412 
 PHE   0.028   0.002   PHE A 511 
 TRP   0.026   0.002   TRP A 373 
 HIS   0.005   0.001   HIS B 499 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 8637)
  covalent geometry    : angle       0.62743 (11823)
  SS BOND              : bond        0.00965 (    2)
  SS BOND              : angle       1.55568 (    4)
  hydrogen bonds       : bond        0.04286 (  667)
  hydrogen bonds       : angle       3.58761 ( 2001)

*********************** 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: 28
    poor density    : 141
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
REVERT: A  294 GLN cc_start: 0.6601 (tm-30) cc_final: 0.6226 (tm-30)
REVERT: A  585 LEU cc_start: 0.4490 (mt) cc_final: 0.4275 (tp)
REVERT: B  244 PHE cc_start: 0.8149 (t80) cc_final: 0.7224 (t80)
REVERT: B  409 ASP cc_start: 0.6304 (p0) cc_final: 0.6033 (p0)
  outliers start: 28
  outliers final: 26
  residues processed: 158
  average time/residue: 0.0649
  time to fit residues: 16.0410
Evaluate side-chains
  162 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 136
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
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  284 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  408 MET
Chi-restraints excluded: chain B residue  474 PHE
Chi-restraints excluded: chain B residue  496 TYR
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 74 optimal weight:   10.0000
   chunk 54 optimal weight:    0.1980
   chunk 96 optimal weight:    0.0670
   chunk 79 optimal weight:    0.7980
   chunk 4 optimal weight:   50.0000
   chunk 12 optimal weight:    0.7980
   chunk 84 optimal weight:    0.1980
   chunk 58 optimal weight:   50.0000
   chunk 18 optimal weight:   10.0000
   chunk 80 optimal weight:    0.7980
   chunk 22 optimal weight:    0.5980
   overall best weight:    0.3718

-------------------------------------------------------------------------------
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 = 0.199952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.157029 restraints weight = 17807.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.153698 restraints weight = 10944.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.154661 restraints weight = 10991.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.154907 restraints weight = 8668.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.155117 restraints weight = 7932.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.4072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7068
moved from start:          0.2917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8639  Z= 0.125
  Angle     :  0.616   9.963  11827  Z= 0.323
  Chirality :  0.038   0.141   1375
  Planarity :  0.004   0.069   1499
  Dihedral  :  3.722  17.484   1239
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.99 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 26.78 %
    Favored  : 69.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.59 (0.26), residues: 1153
  helix:  2.74 (0.17), residues: 874
  sheet:  None (None), residues: 0
  loop : -1.87 (0.36), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 465 
 TYR   0.032   0.001   TYR B 412 
 PHE   0.019   0.001   PHE A 546 
 TRP   0.033   0.002   TRP A 373 
 HIS   0.018   0.001   HIS B 504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 8637)
  covalent geometry    : angle       0.61557 (11823)
  SS BOND              : bond        0.00728 (    2)
  SS BOND              : angle       1.15133 (    4)
  hydrogen bonds       : bond        0.03816 (  667)
  hydrogen bonds       : angle       3.51132 ( 2001)

********************** 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
  173 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 148
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
REVERT: A  294 GLN cc_start: 0.6686 (tm-30) cc_final: 0.6339 (tm-30)
REVERT: B  244 PHE cc_start: 0.8176 (t80) cc_final: 0.7224 (t80)
REVERT: B  409 ASP cc_start: 0.6234 (p0) cc_final: 0.5929 (p0)
REVERT: B  504 HIS cc_start: 0.6688 (t-90) cc_final: 0.6358 (t-90)
  outliers start: 25
  outliers final: 24
  residues processed: 162
  average time/residue: 0.0616
  time to fit residues: 15.6343
Evaluate side-chains
  158 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 134
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
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  284 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  408 MET
Chi-restraints excluded: chain B residue  474 PHE
Chi-restraints excluded: chain B residue  496 TYR
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 60 optimal weight:   40.0000
   chunk 8 optimal weight:    5.9990
   chunk 64 optimal weight:    6.9990
   chunk 1 optimal weight:    7.9990
   chunk 88 optimal weight:    0.9990
   chunk 89 optimal weight:    0.8980
   chunk 81 optimal weight:    0.8980
   chunk 9 optimal weight:   50.0000
   chunk 33 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 69 optimal weight:   50.0000
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
B 294 GLN
B 499 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4547 r_free = 0.4547 target = 0.193541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.151403 restraints weight = 17812.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.148364 restraints weight = 12005.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.148937 restraints weight = 10575.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.149367 restraints weight = 8455.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.149265 restraints weight = 7981.728|
|-----------------------------------------------------------------------------|
r_work (final): 0.4014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7125
moved from start:          0.3224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.086   8639  Z= 0.205
  Angle     :  0.685  15.509  11827  Z= 0.360
  Chirality :  0.042   0.191   1375
  Planarity :  0.004   0.070   1499
  Dihedral  :  3.939  20.453   1239
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.42 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 27.78 %
    Favored  : 68.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.27 (0.25), residues: 1153
  helix:  2.47 (0.17), residues: 873
  sheet:  None (None), residues: 0
  loop : -1.81 (0.36), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 459 
 TYR   0.025   0.002   TYR B 412 
 PHE   0.026   0.002   PHE A 511 
 TRP   0.027   0.003   TRP A 373 
 HIS   0.006   0.002   HIS B 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 ( 8637)
  covalent geometry    : angle       0.68506 (11823)
  SS BOND              : bond        0.00923 (    2)
  SS BOND              : angle       1.38852 (    4)
  hydrogen bonds       : bond        0.04579 (  667)
  hydrogen bonds       : angle       3.77676 ( 2001)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1624.77 seconds
wall clock time: 28 minutes 41.39 seconds (1721.39 seconds total)