Starting phenix.real_space_refine
on Wed Sep 17 11:52:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yfu_39230/09_2025/8yfu_39230.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yfu_39230/09_2025/8yfu_39230.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yfu_39230/09_2025/8yfu_39230.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yfu_39230/09_2025/8yfu_39230.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yfu_39230/09_2025/8yfu_39230.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yfu_39230/09_2025/8yfu_39230.map"
  }
  resolution = 4.59
  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=   0.041
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 17 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: 2.10, per 1000 atoms: 0.25
  Number of scatterers: 8419
  At special positions: 0
  Unit cell: (123.2, 126.5, 128.7, 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: 0.84
  Conformation dependent library (CDL) restraints added in 379.2 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:
      43 helices and 0 sheets defined
      79.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  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: 4.113A  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: 3.613A  pdb=" N   GLN A 193 " --> pdb=" O   LYS A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 218
      removed outlier: 3.604A  pdb=" N   ALA A 214 " --> pdb=" O   ASP A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 258
      removed outlier: 3.847A  pdb=" N   THR A 234 " --> pdb=" O   PRO A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 296
      removed outlier: 3.563A  pdb=" N   ILE A 269 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 5.116A  pdb=" N   GLY A 274 " --> pdb=" O   ARG A 270 " (cutoff:3.500A)
      removed outlier: 5.753A  pdb=" N   GLY A 275 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   GLY A 296 " --> pdb=" O   TRP A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 304
    Processing helix  chain 'A' and resid 312 through 337
      removed outlier: 3.712A  pdb=" N   LEU A 316 " --> pdb=" O   SER A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 360
      removed outlier: 4.377A  pdb=" N   LEU A 349 " --> pdb=" O   TYR A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 383
    Processing helix  chain 'A' and resid 390 through 402
      removed outlier: 3.625A  pdb=" N   SER A 402 " --> pdb=" O   ASP A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 419
      removed outlier: 3.907A  pdb=" N   LEU A 407 " --> pdb=" O   LEU A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 471
      removed outlier: 3.945A  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 501
      removed outlier: 4.119A  pdb=" N   THR A 486 " --> pdb=" O   LYS A 482 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   PHE A 487 " --> pdb=" O   TYR A 483 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   PHE A 488 " --> pdb=" O   SER A 484 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   GLU A 501 " --> pdb=" O   SER A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 532
      removed outlier: 4.067A  pdb=" N   PHE A 510 " --> pdb=" O   ASP A 506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 556 through 571
      removed outlier: 4.047A  pdb=" N   PHE A 571 " --> pdb=" O   VAL A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 571 through 581
      removed outlier: 3.938A  pdb=" N   ILE A 575 " --> pdb=" O   PHE A 571 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   GLN A 576 " --> pdb=" O   ALA A 572 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 616
      removed outlier: 4.457A  pdb=" N   ILE A 591 " --> pdb=" O   HIS A 587 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   THR A 594 " --> pdb=" O   ASP A 590 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   VAL A 595 " --> pdb=" O   ILE A 591 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   PHE A 596 " --> pdb=" O   ILE A 592 " (cutoff:3.500A)
      Proline residue:  A 598  - end of helix
      removed outlier: 4.365A  pdb=" N   VAL A 601 " --> pdb=" O   ALA A 597 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   PHE A 602 " --> pdb=" O   PRO A 598 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   PHE A 609 " --> pdb=" O   PHE A 605 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   PHE A 610 " --> pdb=" O   VAL A 606 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LEU A 612 " --> pdb=" O   ASN A 608 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   GLU A 613 " --> pdb=" O   PHE A 609 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 27 through 36
      removed outlier: 4.026A  pdb=" N   GLN B  33 " --> pdb=" O   LEU B  29 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   ALA B  36 " --> pdb=" O   ALA B  32 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 43 through 100
      removed outlier: 3.573A  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: 3.520A  pdb=" N   THR B 187 " --> pdb=" O   ALA B 183 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 206
    Processing helix  chain 'B' and resid 210 through 218
    Processing helix  chain 'B' and resid 230 through 258
      removed outlier: 3.522A  pdb=" N   THR B 234 " --> pdb=" O   PRO B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 265 through 296
      removed outlier: 4.623A  pdb=" N   GLY B 274 " --> pdb=" O   ARG B 270 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   GLY B 275 " --> pdb=" O   ILE B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 303
      removed outlier: 3.999A  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 343 through 345
      No H-bonds generated for 'chain 'B' and resid 343 through 345'
    Processing helix  chain 'B' and resid 346 through 360
      removed outlier: 4.108A  pdb=" N   ALA B 350 " --> pdb=" O   VAL B 346 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   LEU B 351 " --> pdb=" O   TYR B 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 384
      removed outlier: 3.580A  pdb=" N   ARG B 371 " --> pdb=" O   TYR B 367 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   PHE B 372 " --> pdb=" O   TYR B 368 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   THR B 383 " --> pdb=" O   PHE B 379 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   ALA B 384 " --> pdb=" O   ARG B 380 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 390 through 403
      removed outlier: 3.637A  pdb=" N   SER B 402 " --> pdb=" O   ASP B 398 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 420
      removed outlier: 3.760A  pdb=" N   MET B 408 " --> pdb=" O   SER B 404 " (cutoff:3.500A)
      removed outlier: 4.859A  pdb=" N   LEU B 410 " --> pdb=" O   ILE B 406 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   GLU B 411 " --> pdb=" O   LEU B 407 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 471
      Proline residue:  B 455  - end of helix
    Processing helix  chain 'B' and resid 473 through 501
      removed outlier: 3.816A  pdb=" N   GLY B 481 " --> pdb=" O   LEU B 477 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   THR B 486 " --> pdb=" O   LYS B 482 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   PHE B 487 " --> pdb=" O   TYR B 483 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   GLU B 501 " --> pdb=" O   SER B 497 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 532
      removed outlier: 3.727A  pdb=" N   PHE B 511 " --> pdb=" O   THR B 507 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   TYR B 512 " --> pdb=" O   MET B 508 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU B 513 " --> pdb=" O   VAL B 509 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   VAL B 516 " --> pdb=" O   TYR B 512 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   SER B 521 " --> pdb=" O   PHE B 517 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   TYR B 524 " --> pdb=" O   ILE B 520 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LYS B 531 " --> pdb=" O   ILE B 527 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   MET B 532 " --> pdb=" O   TRP B 528 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 555 through 571
      removed outlier: 3.939A  pdb=" N   TYR B 559 " --> pdb=" O   GLN B 555 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   PHE B 571 " --> pdb=" O   VAL B 567 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 573 through 580
      removed outlier: 3.588A  pdb=" N   ILE B 577 " --> pdb=" O   TRP B 573 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 588 through 620
      removed outlier: 4.112A  pdb=" N   ILE B 592 " --> pdb=" O   SER B 588 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   ALA B 593 " --> pdb=" O   GLY B 589 " (cutoff:3.500A)
      Proline residue:  B 598  - end of helix
      removed outlier: 3.629A  pdb=" N   VAL B 601 " --> pdb=" O   ALA B 597 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ARG B 604 " --> pdb=" O   GLU B 600 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   PHE B 605 " --> pdb=" O   VAL B 601 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   VAL B 606 " --> pdb=" O   PHE B 602 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   TRP B 607 " --> pdb=" O   ARG B 603 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   PHE B 609 " --> pdb=" O   PHE B 605 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   PHE B 610 " --> pdb=" O   VAL B 606 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLU B 615 " --> pdb=" O   ARG B 611 " (cutoff:3.500A)

    662 hydrogen bonds defined for protein.
    1980 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: 1.33

  Time building geometry restraints manager: 1.08 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: 2382
        1.34 -     1.46: 1609
        1.46 -     1.58: 4602
        1.58 -     1.69: 0
        1.69 -     1.81: 44
  Bond restraints: 8637
  Sorted by residual:
  bond pdb=" CA  VAL A 220 "
       pdb=" CB  VAL A 220 "
    ideal  model  delta    sigma   weight residual
    1.539  1.549 -0.010 5.40e-03 3.43e+04 3.16e+00
  bond pdb=" CG1 ILE B 249 "
       pdb=" CD1 ILE B 249 "
    ideal  model  delta    sigma   weight residual
    1.513  1.459  0.054 3.90e-02 6.57e+02 1.91e+00
  bond pdb=" CB  TRP A 395 "
       pdb=" CG  TRP A 395 "
    ideal  model  delta    sigma   weight residual
    1.498  1.538 -0.040 3.10e-02 1.04e+03 1.67e+00
  bond pdb=" C   ALA B 384 "
       pdb=" N   PRO B 385 "
    ideal  model  delta    sigma   weight residual
    1.335  1.351 -0.016 1.28e-02 6.10e+03 1.62e+00
  bond pdb=" C   ALA A 226 "
       pdb=" N   GLN A 227 "
    ideal  model  delta    sigma   weight residual
    1.329  1.345 -0.016 1.40e-02 5.10e+03 1.24e+00
  ... (remaining 8632 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.65: 11796
        4.65 -     9.31: 26
        9.31 -    13.96: 0
       13.96 -    18.61: 0
       18.61 -    23.27: 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  144.97  -23.27 1.80e+00 3.09e-01 1.67e+02
  angle pdb=" N   VAL A 341 "
        pdb=" CA  VAL A 341 "
        pdb=" C   VAL A 341 "
      ideal   model   delta    sigma   weight residual
     112.12  108.54    3.58 8.40e-01 1.42e+00 1.82e+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  130.99   -9.19 2.44e+00 1.68e-01 1.42e+01
  angle pdb=" C   ALA A 225 "
        pdb=" N   ALA A 226 "
        pdb=" CA  ALA A 226 "
      ideal   model   delta    sigma   weight residual
     121.54  128.27   -6.73 1.91e+00 2.74e-01 1.24e+01
  angle pdb=" CA  ALA A 226 "
        pdb=" C   ALA A 226 "
        pdb=" N   GLN A 227 "
      ideal   model   delta    sigma   weight residual
     116.84  122.00   -5.16 1.71e+00 3.42e-01 9.11e+00
  ... (remaining 11818 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 4572
       17.93 -    35.86: 319
       35.86 -    53.79: 55
       53.79 -    71.72: 4
       71.72 -    89.65: 5
  Dihedral angle restraints: 4955
    sinusoidal: 1526
      harmonic: 3429
  Sorted by residual:
  dihedral pdb=" CA  ALA B 473 "
           pdb=" C   ALA B 473 "
           pdb=" N   PHE B 474 "
           pdb=" CA  PHE B 474 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.49  -18.51     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" CA  SER B 521 "
           pdb=" C   SER B 521 "
           pdb=" N   SER B 522 "
           pdb=" CA  SER B 522 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.27  -15.73     0      5.00e+00 4.00e-02 9.90e+00
  dihedral pdb=" CA  ILE A 342 "
           pdb=" C   ILE A 342 "
           pdb=" N   PRO A 343 "
           pdb=" CA  PRO A 343 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.48  -15.52     0      5.00e+00 4.00e-02 9.64e+00
  ... (remaining 4952 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 959
       0.035 -    0.070: 320
       0.070 -    0.105: 82
       0.105 -    0.140: 11
       0.140 -    0.175: 3
  Chirality restraints: 1375
  Sorted by residual:
  chirality pdb=" CA  ALA A 226 "
            pdb=" N   ALA A 226 "
            pdb=" C   ALA A 226 "
            pdb=" CB  ALA A 226 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.31    0.18 2.00e-01 2.50e+01 7.67e-01
  chirality pdb=" CA  ALA B 384 "
            pdb=" N   ALA B 384 "
            pdb=" C   ALA B 384 "
            pdb=" CB  ALA B 384 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.34    0.14 2.00e-01 2.50e+01 5.14e-01
  chirality pdb=" CB  THR A 261 "
            pdb=" CA  THR A 261 "
            pdb=" OG1 THR A 261 "
            pdb=" CG2 THR A 261 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.41    0.14 2.00e-01 2.50e+01 5.08e-01
  ... (remaining 1372 not shown)

  Planarity restraints: 1499
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 395 "   -0.020 2.00e-02 2.50e+03   2.09e-02 1.09e+01
        pdb=" CG  TRP A 395 "    0.053 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 395 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 395 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 395 "    0.009 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 395 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 395 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 395 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 395 "   -0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 395 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 517 "   -0.015 2.00e-02 2.50e+03   1.48e-02 3.85e+00
        pdb=" CG  PHE A 517 "    0.034 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 517 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 517 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 517 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 517 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 517 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 306 "   -0.030 5.00e-02 4.00e+02   4.63e-02 3.43e+00
        pdb=" N   PRO B 307 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO B 307 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 307 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1496 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 81
        2.64 -     3.21: 8597
        3.21 -     3.77: 13329
        3.77 -     4.34: 15878
        4.34 -     4.90: 25350
  Nonbonded interactions: 63235
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 575 "
            pdb=" OG  SER A 578 "
     model   vdw
     2.081 3.040
  nonbonded pdb=" OG  SER B 402 "
            pdb=" NH2 ARG B 604 "
     model   vdw
     2.151 3.120
  nonbonded pdb=" O   HIS A 387 "
            pdb=" NH1 ARG A 465 "
     model   vdw
     2.152 3.120
  nonbonded pdb=" O   TYR B 518 "
            pdb=" OG  SER B 521 "
     model   vdw
     2.159 3.040
  nonbonded pdb=" O   ALA A 384 "
            pdb=" NH1 ARG A 465 "
     model   vdw
     2.161 3.120
  ... (remaining 63230 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:             2.170
  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:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.480
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7170
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      :  0.003   0.055   8639  Z= 0.147
  Angle     :  0.672  23.267  11827  Z= 0.370
  Chirality :  0.038   0.175   1375
  Planarity :  0.004   0.046   1499
  Dihedral  : 12.845  89.649   2719
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.29 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  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:  1.47 (0.26), residues: 1153
  helix:  2.05 (0.18), residues: 843
  sheet:  None (None), residues: 0
  loop : -2.22 (0.37), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 604 
 TYR   0.017   0.001   TYR B 345 
 PHE   0.034   0.001   PHE A 517 
 TRP   0.053   0.002   TRP A 395 
 HIS   0.010   0.001   HIS B 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 8637)
  covalent geometry    : angle       0.67151 (11823)
  SS BOND              : bond        0.00189 (    2)
  SS BOND              : angle       0.75516 (    4)
  hydrogen bonds       : bond        0.13070 (  662)
  hydrogen bonds       : angle       5.54392 ( 1980)

*********************** 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
  182 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  284 LEU cc_start: 0.9315 (mt) cc_final: 0.9098 (mt)
REVERT: A  318 GLU cc_start: 0.8482 (pp20) cc_final: 0.8216 (pp20)
REVERT: A  319 ILE cc_start: 0.8491 (mt) cc_final: 0.8285 (mt)
REVERT: A  413 MET cc_start: 0.8920 (ppp) cc_final: 0.8573 (ppp)
REVERT: A  508 MET cc_start: 0.6607 (mmt) cc_final: 0.6158 (mmt)
REVERT: A  558 TYR cc_start: 0.8090 (m-80) cc_final: 0.7773 (m-80)
REVERT: B  241 CYS cc_start: 0.8770 (t) cc_final: 0.8495 (t)
REVERT: B  248 ASN cc_start: 0.9206 (t0) cc_final: 0.8952 (t0)
REVERT: B  280 GLU cc_start: 0.9164 (tt0) cc_final: 0.8508 (tp30)
REVERT: B  281 PHE cc_start: 0.8803 (t80) cc_final: 0.8603 (t80)
REVERT: B  288 ASN cc_start: 0.9278 (m110) cc_final: 0.8766 (m-40)
REVERT: B  403 LEU cc_start: 0.9108 (mt) cc_final: 0.8887 (mt)
REVERT: B  411 GLU cc_start: 0.9493 (tm-30) cc_final: 0.9147 (tm-30)
REVERT: B  524 TYR cc_start: 0.7476 (t80) cc_final: 0.7192 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.0727
  time to fit residues: 19.8721
Evaluate side-chains
  146 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.0980
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:   40.0000
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:   40.0000
   chunk 51 optimal weight:    9.9990
   chunk 100 optimal weight:    5.9990
   overall best weight:    2.0186

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

Flipped N/Q/H residues before XYZ refinement:
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 387 HIS
** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 619 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.134502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.103849 restraints weight = 26980.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.106473 restraints weight = 16287.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.108241 restraints weight = 11510.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.109165 restraints weight = 9060.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.109454 restraints weight = 7817.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7201
moved from start:          0.1319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8639  Z= 0.198
  Angle     :  0.643  11.985  11827  Z= 0.349
  Chirality :  0.039   0.260   1375
  Planarity :  0.004   0.055   1499
  Dihedral  :  4.034  20.947   1239
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 12.34
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.94 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  7.12 %
    Favored  : 92.59 %
  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:  1.64 (0.26), residues: 1153
  helix:  2.12 (0.17), residues: 854
  sheet:  None (None), residues: 0
  loop : -2.15 (0.38), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 459 
 TYR   0.042   0.002   TYR B 558 
 PHE   0.024   0.002   PHE A 517 
 TRP   0.023   0.002   TRP A 395 
 HIS   0.008   0.001   HIS B 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 8637)
  covalent geometry    : angle       0.64303 (11823)
  SS BOND              : bond        0.00410 (    2)
  SS BOND              : angle       1.11236 (    4)
  hydrogen bonds       : bond        0.04461 (  662)
  hydrogen bonds       : angle       4.11049 ( 1980)

*********************** 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: 2
    poor density    : 180
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  284 LEU cc_start: 0.9207 (mt) cc_final: 0.8841 (mt)
REVERT: A  287 ILE cc_start: 0.9474 (mp) cc_final: 0.9218 (tp)
REVERT: A  359 LEU cc_start: 0.9305 (tt) cc_final: 0.9096 (tt)
REVERT: A  413 MET cc_start: 0.8900 (ppp) cc_final: 0.8503 (ppp)
REVERT: A  508 MET cc_start: 0.6815 (mmt) cc_final: 0.6149 (mmp)
REVERT: A  558 TYR cc_start: 0.8063 (m-80) cc_final: 0.7780 (m-80)
REVERT: A  565 GLU cc_start: 0.9278 (tm-30) cc_final: 0.9030 (tp30)
REVERT: A  600 GLU cc_start: 0.8646 (mp0) cc_final: 0.8029 (mm-30)
REVERT: B  241 CYS cc_start: 0.8823 (t) cc_final: 0.8585 (t)
REVERT: B  248 ASN cc_start: 0.9235 (t0) cc_final: 0.8904 (t0)
REVERT: B  280 GLU cc_start: 0.9179 (tt0) cc_final: 0.8601 (tp30)
REVERT: B  288 ASN cc_start: 0.9358 (m110) cc_final: 0.9072 (t0)
REVERT: B  328 CYS cc_start: 0.8970 (m) cc_final: 0.8757 (m)
REVERT: B  403 LEU cc_start: 0.8862 (mt) cc_final: 0.8651 (mt)
REVERT: B  411 GLU cc_start: 0.9488 (tm-30) cc_final: 0.9120 (tm-30)
REVERT: B  496 TYR cc_start: 0.8328 (t80) cc_final: 0.8120 (t80)
REVERT: B  509 VAL cc_start: 0.9187 (t) cc_final: 0.8945 (t)
REVERT: B  510 PHE cc_start: 0.8009 (m-10) cc_final: 0.7674 (m-10)
REVERT: B  610 PHE cc_start: 0.9045 (m-10) cc_final: 0.8815 (m-10)
  outliers start: 2
  outliers final: 0
  residues processed: 181
  average time/residue: 0.0656
  time to fit residues: 18.1468
Evaluate side-chains
  142 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 84 optimal weight:    3.9990
   chunk 39 optimal weight:    8.9990
   chunk 54 optimal weight:    8.9990
   chunk 49 optimal weight:    0.4980
   chunk 37 optimal weight:    0.9990
   chunk 106 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 61 optimal weight:   50.0000
   chunk 7 optimal weight:    8.9990
   chunk 97 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0040
   overall best weight:    1.0396

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

Flipped N/Q/H residues before XYZ refinement:
** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 387 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.136455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.105629 restraints weight = 26145.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.108252 restraints weight = 15955.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.110094 restraints weight = 11326.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.111034 restraints weight = 8916.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.112160 restraints weight = 7683.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7128
moved from start:          0.1585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8639  Z= 0.136
  Angle     :  0.587  11.674  11827  Z= 0.315
  Chirality :  0.038   0.243   1375
  Planarity :  0.004   0.056   1499
  Dihedral  :  3.888  21.232   1239
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.51 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  3.85 %
    Favored  : 95.87 %
  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:  1.90 (0.26), residues: 1153
  helix:  2.32 (0.17), residues: 858
  sheet:  None (None), residues: 0
  loop : -2.14 (0.38), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 270 
 TYR   0.017   0.001   TYR B 558 
 PHE   0.020   0.001   PHE A 235 
 TRP   0.019   0.001   TRP A 395 
 HIS   0.006   0.001   HIS B 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 8637)
  covalent geometry    : angle       0.58623 (11823)
  SS BOND              : bond        0.00343 (    2)
  SS BOND              : angle       1.20581 (    4)
  hydrogen bonds       : bond        0.04135 (  662)
  hydrogen bonds       : angle       3.77834 ( 1980)

*********************** 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
  192 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 190
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 PHE cc_start: 0.9136 (t80) cc_final: 0.8907 (t80)
REVERT: A  292 TRP cc_start: 0.7842 (m-10) cc_final: 0.7613 (m-10)
REVERT: A  394 PHE cc_start: 0.8092 (p90) cc_final: 0.7643 (p90)
REVERT: A  413 MET cc_start: 0.8962 (ppp) cc_final: 0.8624 (ppp)
REVERT: A  508 MET cc_start: 0.6619 (mmt) cc_final: 0.5755 (mmp)
REVERT: A  558 TYR cc_start: 0.7889 (m-80) cc_final: 0.7565 (m-80)
REVERT: A  565 GLU cc_start: 0.9262 (tm-30) cc_final: 0.8965 (tp30)
REVERT: A  600 GLU cc_start: 0.8628 (mp0) cc_final: 0.8054 (mm-30)
REVERT: A  607 TRP cc_start: 0.8260 (t60) cc_final: 0.7577 (t60)
REVERT: B  241 CYS cc_start: 0.8768 (t) cc_final: 0.8493 (t)
REVERT: B  248 ASN cc_start: 0.9236 (t0) cc_final: 0.8890 (t0)
REVERT: B  280 GLU cc_start: 0.9098 (tt0) cc_final: 0.8708 (tp30)
REVERT: B  328 CYS cc_start: 0.8963 (m) cc_final: 0.8719 (m)
REVERT: B  411 GLU cc_start: 0.9448 (tm-30) cc_final: 0.9162 (tm-30)
REVERT: B  489 MET cc_start: 0.8298 (ttt) cc_final: 0.8049 (ttt)
REVERT: B  509 VAL cc_start: 0.9178 (t) cc_final: 0.8911 (t)
  outliers start: 2
  outliers final: 0
  residues processed: 190
  average time/residue: 0.0730
  time to fit residues: 20.7872
Evaluate side-chains
  143 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 90 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   chunk 47 optimal weight:    5.9990
   chunk 74 optimal weight:    8.9990
   chunk 76 optimal weight:    0.0770
   chunk 89 optimal weight:    0.9990
   chunk 0 optimal weight:   40.0000
   chunk 55 optimal weight:    0.3980
   chunk 58 optimal weight:   20.0000
   overall best weight:    0.6540

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

Flipped N/Q/H residues before XYZ refinement:
** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 298 ASN
B 387 HIS
B 504 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.137569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.106614 restraints weight = 26350.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.109484 restraints weight = 15458.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.111396 restraints weight = 10665.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.112556 restraints weight = 8279.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.113586 restraints weight = 6989.911|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7091
moved from start:          0.1847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049   8639  Z= 0.123
  Angle     :  0.578  11.039  11827  Z= 0.304
  Chirality :  0.038   0.238   1375
  Planarity :  0.003   0.060   1499
  Dihedral  :  3.840  19.714   1239
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.51 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  3.99 %
    Favored  : 95.73 %
  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:  2.00 (0.26), residues: 1153
  helix:  2.41 (0.17), residues: 858
  sheet:  None (None), residues: 0
  loop : -2.17 (0.38), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 604 
 TYR   0.013   0.001   TYR B 558 
 PHE   0.018   0.001   PHE B 609 
 TRP   0.019   0.001   TRP B 292 
 HIS   0.006   0.001   HIS B 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 8637)
  covalent geometry    : angle       0.57774 (11823)
  SS BOND              : bond        0.00294 (    2)
  SS BOND              : angle       1.05538 (    4)
  hydrogen bonds       : bond        0.03786 (  662)
  hydrogen bonds       : angle       3.63437 ( 1980)

*********************** 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
  186 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 184
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 PHE cc_start: 0.9120 (t80) cc_final: 0.8849 (t80)
REVERT: A  413 MET cc_start: 0.9034 (ppp) cc_final: 0.8658 (ppp)
REVERT: A  508 MET cc_start: 0.6570 (mmt) cc_final: 0.5825 (mmp)
REVERT: A  558 TYR cc_start: 0.7836 (m-80) cc_final: 0.7520 (m-80)
REVERT: A  565 GLU cc_start: 0.9231 (tm-30) cc_final: 0.8979 (tp30)
REVERT: A  600 GLU cc_start: 0.8668 (mp0) cc_final: 0.8036 (mm-30)
REVERT: B  241 CYS cc_start: 0.8830 (t) cc_final: 0.8545 (t)
REVERT: B  248 ASN cc_start: 0.9252 (t0) cc_final: 0.8875 (t0)
REVERT: B  280 GLU cc_start: 0.9197 (tt0) cc_final: 0.8636 (tp30)
REVERT: B  281 PHE cc_start: 0.8825 (t80) cc_final: 0.8584 (t80)
REVERT: B  328 CYS cc_start: 0.8963 (m) cc_final: 0.8702 (m)
REVERT: B  403 LEU cc_start: 0.8956 (mt) cc_final: 0.8739 (mt)
REVERT: B  411 GLU cc_start: 0.9472 (tm-30) cc_final: 0.9185 (tm-30)
REVERT: B  509 VAL cc_start: 0.9215 (t) cc_final: 0.8968 (t)
REVERT: B  605 PHE cc_start: 0.8600 (t80) cc_final: 0.8327 (t80)
  outliers start: 2
  outliers final: 0
  residues processed: 185
  average time/residue: 0.0650
  time to fit residues: 18.6179
Evaluate side-chains
  144 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 113 optimal weight:    0.0370
   chunk 32 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9980
   chunk 18 optimal weight:    0.0050
   chunk 89 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 98 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   chunk 65 optimal weight:    5.9990
   chunk 43 optimal weight:    0.0470
   chunk 40 optimal weight:    3.9990
   overall best weight:    0.3970

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

Flipped N/Q/H residues before XYZ refinement:
** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 499 HIS
B 387 HIS
B 504 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.139205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.108276 restraints weight = 25448.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.111069 restraints weight = 15552.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.112890 restraints weight = 10941.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.114157 restraints weight = 8598.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.115100 restraints weight = 7269.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7073
moved from start:          0.2074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8639  Z= 0.114
  Angle     :  0.558  10.314  11827  Z= 0.294
  Chirality :  0.038   0.238   1375
  Planarity :  0.004   0.064   1499
  Dihedral  :  3.759  18.613   1239
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.16 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  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:  2.11 (0.26), residues: 1153
  helix:  2.49 (0.17), residues: 861
  sheet:  None (None), residues: 0
  loop : -2.16 (0.37), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 604 
 TYR   0.026   0.001   TYR A 512 
 PHE   0.021   0.001   PHE A 235 
 TRP   0.024   0.001   TRP A 534 
 HIS   0.006   0.001   HIS B 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 ( 8637)
  covalent geometry    : angle       0.55770 (11823)
  SS BOND              : bond        0.00320 (    2)
  SS BOND              : angle       1.07466 (    4)
  hydrogen bonds       : bond        0.03497 (  662)
  hydrogen bonds       : angle       3.58942 ( 1980)

*********************** 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
  193 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 PHE cc_start: 0.9102 (t80) cc_final: 0.8800 (t80)
REVERT: A  284 LEU cc_start: 0.9071 (mt) cc_final: 0.8853 (mt)
REVERT: A  287 ILE cc_start: 0.9390 (mp) cc_final: 0.9180 (tp)
REVERT: A  318 GLU cc_start: 0.8417 (pp20) cc_final: 0.7826 (pp20)
REVERT: A  394 PHE cc_start: 0.8003 (p90) cc_final: 0.7524 (p90)
REVERT: A  408 MET cc_start: 0.8538 (ttt) cc_final: 0.8126 (ttt)
REVERT: A  413 MET cc_start: 0.8989 (ppp) cc_final: 0.8643 (ppp)
REVERT: A  508 MET cc_start: 0.6459 (mmt) cc_final: 0.5839 (mmp)
REVERT: A  512 TYR cc_start: 0.8480 (m-80) cc_final: 0.8235 (m-10)
REVERT: A  524 TYR cc_start: 0.8052 (t80) cc_final: 0.7799 (t80)
REVERT: A  558 TYR cc_start: 0.7756 (m-80) cc_final: 0.7502 (m-80)
REVERT: A  565 GLU cc_start: 0.9191 (tm-30) cc_final: 0.8956 (tp30)
REVERT: A  566 ASP cc_start: 0.9120 (t0) cc_final: 0.8919 (t0)
REVERT: A  600 GLU cc_start: 0.8639 (mp0) cc_final: 0.8009 (mm-30)
REVERT: B  241 CYS cc_start: 0.8799 (t) cc_final: 0.8536 (t)
REVERT: B  248 ASN cc_start: 0.9227 (t0) cc_final: 0.8824 (t0)
REVERT: B  280 GLU cc_start: 0.9220 (tt0) cc_final: 0.8709 (tp30)
REVERT: B  281 PHE cc_start: 0.8766 (t80) cc_final: 0.8540 (t80)
REVERT: B  328 CYS cc_start: 0.8893 (m) cc_final: 0.8632 (m)
REVERT: B  403 LEU cc_start: 0.8924 (mt) cc_final: 0.8703 (mt)
REVERT: B  408 MET cc_start: 0.9043 (pmm) cc_final: 0.8759 (pmm)
REVERT: B  411 GLU cc_start: 0.9434 (tm-30) cc_final: 0.8992 (tm-30)
REVERT: B  489 MET cc_start: 0.8112 (ttt) cc_final: 0.7826 (ttt)
REVERT: B  509 VAL cc_start: 0.9193 (t) cc_final: 0.8944 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 193
  average time/residue: 0.0633
  time to fit residues: 18.9544
Evaluate side-chains
  151 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 87 optimal weight:    4.9990
   chunk 69 optimal weight:    6.9990
   chunk 31 optimal weight:    0.7980
   chunk 99 optimal weight:    0.8980
   chunk 112 optimal weight:    8.9990
   chunk 22 optimal weight:    5.9990
   chunk 44 optimal weight:    5.9990
   chunk 59 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   chunk 84 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 288 ASN
B 288 ASN
B 387 HIS
B 504 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.139405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.106169 restraints weight = 25710.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.108801 restraints weight = 16205.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.110416 restraints weight = 11539.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.111661 restraints weight = 9261.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.112636 restraints weight = 7838.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7148
moved from start:          0.2240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8639  Z= 0.122
  Angle     :  0.558   9.517  11827  Z= 0.296
  Chirality :  0.037   0.145   1375
  Planarity :  0.004   0.062   1499
  Dihedral  :  3.768  21.550   1239
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.68 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.71 %
    Favored  : 97.15 %
  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 (0.26), residues: 1153
  helix:  2.53 (0.17), residues: 858
  sheet:  None (None), residues: 0
  loop : -2.01 (0.38), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 459 
 TYR   0.018   0.001   TYR A 512 
 PHE   0.022   0.001   PHE A 235 
 TRP   0.029   0.002   TRP A 395 
 HIS   0.006   0.001   HIS B 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 8637)
  covalent geometry    : angle       0.55755 (11823)
  SS BOND              : bond        0.00329 (    2)
  SS BOND              : angle       1.01285 (    4)
  hydrogen bonds       : bond        0.03432 (  662)
  hydrogen bonds       : angle       3.62671 ( 1980)

*********************** 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
  183 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 182
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
REVERT: A  284 LEU cc_start: 0.9123 (mt) cc_final: 0.8858 (mt)
REVERT: A  287 ILE cc_start: 0.9380 (mp) cc_final: 0.9161 (tp)
REVERT: A  288 ASN cc_start: 0.8650 (OUTLIER) cc_final: 0.7686 (t0)
REVERT: A  413 MET cc_start: 0.9068 (ppp) cc_final: 0.8679 (ppp)
REVERT: A  508 MET cc_start: 0.6427 (mmt) cc_final: 0.5888 (mmp)
REVERT: A  512 TYR cc_start: 0.8527 (m-80) cc_final: 0.8282 (m-10)
REVERT: A  524 TYR cc_start: 0.8081 (t80) cc_final: 0.7841 (t80)
REVERT: A  558 TYR cc_start: 0.7790 (m-80) cc_final: 0.7514 (m-80)
REVERT: A  600 GLU cc_start: 0.8632 (mp0) cc_final: 0.8026 (mm-30)
REVERT: B  241 CYS cc_start: 0.8803 (t) cc_final: 0.8526 (t)
REVERT: B  248 ASN cc_start: 0.9211 (t0) cc_final: 0.8819 (t0)
REVERT: B  280 GLU cc_start: 0.9234 (tt0) cc_final: 0.8794 (tp30)
REVERT: B  281 PHE cc_start: 0.8817 (t80) cc_final: 0.8510 (t80)
REVERT: B  328 CYS cc_start: 0.8880 (m) cc_final: 0.8649 (m)
REVERT: B  408 MET cc_start: 0.9060 (pmm) cc_final: 0.8765 (pmm)
REVERT: B  411 GLU cc_start: 0.9464 (tm-30) cc_final: 0.8991 (tm-30)
REVERT: B  489 MET cc_start: 0.8040 (ttt) cc_final: 0.7710 (ttt)
  outliers start: 1
  outliers final: 0
  residues processed: 183
  average time/residue: 0.0662
  time to fit residues: 18.7332
Evaluate side-chains
  154 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 153
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 17 optimal weight:   10.0000
   chunk 51 optimal weight:    6.9990
   chunk 108 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 61 optimal weight:   50.0000
   chunk 54 optimal weight:    7.9990
   chunk 18 optimal weight:    9.9990
   chunk 88 optimal weight:    8.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
B 504 HIS
B 608 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.134740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.101646 restraints weight = 26554.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.104215 restraints weight = 16727.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.105814 restraints weight = 11997.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.106659 restraints weight = 9653.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.107841 restraints weight = 8409.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7272
moved from start:          0.2646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   8639  Z= 0.217
  Angle     :  0.641  10.110  11827  Z= 0.348
  Chirality :  0.039   0.169   1375
  Planarity :  0.005   0.060   1499
  Dihedral  :  4.016  19.406   1239
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 12.47
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.77 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  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:  1.83 (0.26), residues: 1153
  helix:  2.22 (0.17), residues: 861
  sheet:  None (None), residues: 0
  loop : -2.01 (0.39), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 459 
 TYR   0.017   0.002   TYR A 524 
 PHE   0.020   0.002   PHE A 235 
 TRP   0.033   0.003   TRP A 395 
 HIS   0.008   0.002   HIS B 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 ( 8637)
  covalent geometry    : angle       0.64121 (11823)
  SS BOND              : bond        0.00423 (    2)
  SS BOND              : angle       1.03785 (    4)
  hydrogen bonds       : bond        0.04054 (  662)
  hydrogen bonds       : angle       3.97737 ( 1980)

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

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
REVERT: A  394 PHE cc_start: 0.7864 (p90) cc_final: 0.7366 (p90)
REVERT: A  413 MET cc_start: 0.9044 (ppp) cc_final: 0.8634 (ppp)
REVERT: A  508 MET cc_start: 0.7052 (mmt) cc_final: 0.6183 (mmp)
REVERT: A  512 TYR cc_start: 0.8535 (m-80) cc_final: 0.8253 (m-10)
REVERT: A  558 TYR cc_start: 0.7836 (m-80) cc_final: 0.7452 (m-80)
REVERT: A  565 GLU cc_start: 0.9034 (tp30) cc_final: 0.8678 (tp30)
REVERT: A  566 ASP cc_start: 0.9387 (t0) cc_final: 0.9171 (t0)
REVERT: A  600 GLU cc_start: 0.8769 (mp0) cc_final: 0.8273 (mm-30)
REVERT: B  241 CYS cc_start: 0.8873 (t) cc_final: 0.8620 (t)
REVERT: B  248 ASN cc_start: 0.9265 (t0) cc_final: 0.8891 (t0)
REVERT: B  280 GLU cc_start: 0.9180 (tt0) cc_final: 0.8756 (tp30)
REVERT: B  328 CYS cc_start: 0.8997 (m) cc_final: 0.8740 (m)
REVERT: B  489 MET cc_start: 0.8240 (ttt) cc_final: 0.7867 (ttt)
REVERT: B  509 VAL cc_start: 0.9294 (t) cc_final: 0.8955 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 179
  average time/residue: 0.0607
  time to fit residues: 17.2276
Evaluate side-chains
  144 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:   10.0000
   chunk 33 optimal weight:    0.8980
   chunk 14 optimal weight:    0.2980
   chunk 100 optimal weight:    0.5980
   chunk 55 optimal weight:    0.8980
   chunk 73 optimal weight:   50.0000
   chunk 95 optimal weight:    4.9990
   chunk 102 optimal weight:    0.6980
   chunk 108 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.4214 r_free = 0.4214 target = 0.136822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.106433 restraints weight = 25735.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.109238 restraints weight = 15623.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.110859 restraints weight = 10949.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.112271 restraints weight = 8710.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.113111 restraints weight = 7247.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.3834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7127
moved from start:          0.2730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8639  Z= 0.121
  Angle     :  0.587   9.065  11827  Z= 0.309
  Chirality :  0.038   0.155   1375
  Planarity :  0.004   0.079   1499
  Dihedral  :  3.868  18.772   1239
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.08 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  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:  2.06 (0.26), residues: 1153
  helix:  2.38 (0.17), residues: 863
  sheet:  None (None), residues: 0
  loop : -1.97 (0.39), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 465 
 TYR   0.016   0.001   TYR A 512 
 PHE   0.023   0.001   PHE A 394 
 TRP   0.036   0.002   TRP A 395 
 HIS   0.008   0.001   HIS A 616 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 8637)
  covalent geometry    : angle       0.58655 (11823)
  SS BOND              : bond        0.00340 (    2)
  SS BOND              : angle       1.03427 (    4)
  hydrogen bonds       : bond        0.03651 (  662)
  hydrogen bonds       : angle       3.69255 ( 1980)

*********************** 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
  186 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
REVERT: A  394 PHE cc_start: 0.7820 (p90) cc_final: 0.7293 (p90)
REVERT: A  413 MET cc_start: 0.9035 (ppp) cc_final: 0.8717 (ppp)
REVERT: A  488 PHE cc_start: 0.9027 (m-80) cc_final: 0.8625 (m-80)
REVERT: A  489 MET cc_start: 0.8463 (tpt) cc_final: 0.8234 (tpt)
REVERT: A  492 PHE cc_start: 0.8625 (m-80) cc_final: 0.8157 (m-80)
REVERT: A  508 MET cc_start: 0.6789 (mmt) cc_final: 0.5898 (mmp)
REVERT: A  512 TYR cc_start: 0.8597 (m-80) cc_final: 0.8288 (m-10)
REVERT: A  558 TYR cc_start: 0.7611 (m-80) cc_final: 0.7229 (m-80)
REVERT: A  565 GLU cc_start: 0.9048 (tp30) cc_final: 0.8672 (tp30)
REVERT: A  566 ASP cc_start: 0.9309 (t0) cc_final: 0.8996 (t0)
REVERT: A  600 GLU cc_start: 0.8716 (mp0) cc_final: 0.8041 (mm-30)
REVERT: A  612 LEU cc_start: 0.8744 (tt) cc_final: 0.8500 (tt)
REVERT: B  241 CYS cc_start: 0.8854 (t) cc_final: 0.8597 (t)
REVERT: B  248 ASN cc_start: 0.9259 (t0) cc_final: 0.8871 (t0)
REVERT: B  280 GLU cc_start: 0.9217 (tt0) cc_final: 0.8761 (tp30)
REVERT: B  328 CYS cc_start: 0.8969 (m) cc_final: 0.8724 (m)
REVERT: B  377 LEU cc_start: 0.8574 (mm) cc_final: 0.8247 (mm)
REVERT: B  462 GLN cc_start: 0.9136 (mp10) cc_final: 0.8831 (mp10)
REVERT: B  489 MET cc_start: 0.8122 (ttt) cc_final: 0.7766 (ttt)
REVERT: B  509 VAL cc_start: 0.9323 (t) cc_final: 0.8981 (t)
REVERT: B  533 ASP cc_start: 0.8463 (m-30) cc_final: 0.8194 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 186
  average time/residue: 0.0655
  time to fit residues: 18.7668
Evaluate side-chains
  152 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 97 optimal weight:    6.9990
   chunk 104 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   chunk 72 optimal weight:   20.0000
   chunk 42 optimal weight:    0.8980
   chunk 14 optimal weight:    9.9990
   chunk 81 optimal weight:    0.9990
   chunk 15 optimal weight:    8.9990
   chunk 3 optimal weight:   20.0000
   chunk 9 optimal weight:   30.0000
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 441 HIS
B 504 HIS
B 608 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.135687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.102924 restraints weight = 26110.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.105567 restraints weight = 16239.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.107147 restraints weight = 11593.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.108500 restraints weight = 9297.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.108963 restraints weight = 7880.686|
|-----------------------------------------------------------------------------|
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7229
moved from start:          0.2908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8639  Z= 0.163
  Angle     :  0.622   9.282  11827  Z= 0.332
  Chirality :  0.039   0.191   1375
  Planarity :  0.004   0.059   1499
  Dihedral  :  3.952  19.212   1239
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.46 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  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:  1.98 (0.26), residues: 1153
  helix:  2.33 (0.17), residues: 865
  sheet:  None (None), residues: 0
  loop : -2.05 (0.38), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 465 
 TYR   0.017   0.001   TYR A 512 
 PHE   0.028   0.002   PHE B 382 
 TRP   0.064   0.002   TRP A 292 
 HIS   0.014   0.001   HIS B 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 8637)
  covalent geometry    : angle       0.62137 (11823)
  SS BOND              : bond        0.00351 (    2)
  SS BOND              : angle       1.12152 (    4)
  hydrogen bonds       : bond        0.03771 (  662)
  hydrogen bonds       : angle       3.81026 ( 1980)

*********************** 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
  172 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
REVERT: A  394 PHE cc_start: 0.7807 (p90) cc_final: 0.7283 (p90)
REVERT: A  413 MET cc_start: 0.9093 (ppp) cc_final: 0.8721 (ppp)
REVERT: A  488 PHE cc_start: 0.8966 (m-80) cc_final: 0.8564 (m-80)
REVERT: A  489 MET cc_start: 0.8519 (tpt) cc_final: 0.8224 (tpt)
REVERT: A  492 PHE cc_start: 0.8573 (m-80) cc_final: 0.8104 (m-80)
REVERT: A  508 MET cc_start: 0.6949 (mmt) cc_final: 0.6110 (mmp)
REVERT: A  512 TYR cc_start: 0.8503 (m-80) cc_final: 0.8233 (m-10)
REVERT: A  558 TYR cc_start: 0.7619 (m-80) cc_final: 0.7182 (m-80)
REVERT: A  565 GLU cc_start: 0.9029 (tp30) cc_final: 0.8624 (tp30)
REVERT: A  566 ASP cc_start: 0.9362 (t0) cc_final: 0.8984 (t0)
REVERT: A  600 GLU cc_start: 0.8591 (mp0) cc_final: 0.8160 (mm-30)
REVERT: B  241 CYS cc_start: 0.8871 (t) cc_final: 0.8598 (t)
REVERT: B  248 ASN cc_start: 0.9262 (t0) cc_final: 0.8891 (t0)
REVERT: B  280 GLU cc_start: 0.9191 (tt0) cc_final: 0.8721 (tp30)
REVERT: B  281 PHE cc_start: 0.8809 (t80) cc_final: 0.8423 (t80)
REVERT: B  328 CYS cc_start: 0.8992 (m) cc_final: 0.8745 (m)
REVERT: B  489 MET cc_start: 0.8187 (ttt) cc_final: 0.7797 (ttt)
REVERT: B  509 VAL cc_start: 0.9284 (t) cc_final: 0.8939 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 172
  average time/residue: 0.0610
  time to fit residues: 16.5999
Evaluate side-chains
  138 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0870
   chunk 96 optimal weight:    4.9990
   chunk 79 optimal weight:    7.9990
   chunk 4 optimal weight:   30.0000
   chunk 12 optimal weight:   30.0000
   chunk 84 optimal weight:    1.9990
   chunk 58 optimal weight:   30.0000
   chunk 18 optimal weight:    0.9980
   chunk 80 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   overall best weight:    2.0164

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

Flipped N/Q/H residues before XYZ refinement:
** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.133061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.103246 restraints weight = 26210.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.105894 restraints weight = 16061.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.107317 restraints weight = 11268.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.108802 restraints weight = 9126.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.109288 restraints weight = 7521.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7219
moved from start:          0.3160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8639  Z= 0.192
  Angle     :  0.655  10.225  11827  Z= 0.354
  Chirality :  0.041   0.227   1375
  Planarity :  0.004   0.060   1499
  Dihedral  :  4.132  20.326   1239
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 13.17
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.98 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  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:  1.79 (0.26), residues: 1153
  helix:  2.20 (0.17), residues: 862
  sheet:  None (None), residues: 0
  loop : -2.10 (0.38), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 459 
 TYR   0.017   0.001   TYR A 512 
 PHE   0.021   0.002   PHE A 394 
 TRP   0.036   0.002   TRP A 292 
 HIS   0.007   0.001   HIS A 616 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 8637)
  covalent geometry    : angle       0.65520 (11823)
  SS BOND              : bond        0.00356 (    2)
  SS BOND              : angle       1.11137 (    4)
  hydrogen bonds       : bond        0.04010 (  662)
  hydrogen bonds       : angle       3.95007 ( 1980)

********************** 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: 0
    poor density    : 173
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
REVERT: A  273 ARG cc_start: 0.8900 (ptm160) cc_final: 0.8658 (ptm160)
REVERT: A  394 PHE cc_start: 0.7888 (p90) cc_final: 0.7382 (p90)
REVERT: A  413 MET cc_start: 0.9100 (ppp) cc_final: 0.8850 (ppp)
REVERT: A  488 PHE cc_start: 0.9021 (m-80) cc_final: 0.8597 (m-80)
REVERT: A  489 MET cc_start: 0.8609 (tpt) cc_final: 0.8256 (tpt)
REVERT: A  492 PHE cc_start: 0.8630 (m-80) cc_final: 0.8139 (m-80)
REVERT: A  508 MET cc_start: 0.7098 (mmt) cc_final: 0.6202 (mmp)
REVERT: A  512 TYR cc_start: 0.8670 (m-80) cc_final: 0.8290 (m-10)
REVERT: A  558 TYR cc_start: 0.6865 (m-80) cc_final: 0.6415 (m-80)
REVERT: A  565 GLU cc_start: 0.9123 (tp30) cc_final: 0.8636 (tp30)
REVERT: A  566 ASP cc_start: 0.9363 (t0) cc_final: 0.9042 (t0)
REVERT: A  600 GLU cc_start: 0.8695 (mp0) cc_final: 0.8229 (mm-30)
REVERT: B  241 CYS cc_start: 0.8852 (t) cc_final: 0.8616 (t)
REVERT: B  248 ASN cc_start: 0.9266 (t0) cc_final: 0.8895 (t0)
REVERT: B  280 GLU cc_start: 0.9184 (tt0) cc_final: 0.8651 (tp30)
REVERT: B  281 PHE cc_start: 0.8826 (t80) cc_final: 0.8517 (t80)
REVERT: B  328 CYS cc_start: 0.9086 (m) cc_final: 0.8773 (m)
REVERT: B  334 CYS cc_start: 0.6747 (m) cc_final: 0.6296 (m)
REVERT: B  403 LEU cc_start: 0.8996 (mt) cc_final: 0.8783 (mt)
REVERT: B  462 GLN cc_start: 0.8933 (mp10) cc_final: 0.8621 (mp10)
REVERT: B  489 MET cc_start: 0.8108 (ttt) cc_final: 0.7741 (ttt)
REVERT: B  509 VAL cc_start: 0.9304 (t) cc_final: 0.8951 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.0645
  time to fit residues: 17.3421
Evaluate side-chains
  134 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 60 optimal weight:   30.0000
   chunk 8 optimal weight:   20.0000
   chunk 64 optimal weight:   20.0000
   chunk 1 optimal weight:   40.0000
   chunk 88 optimal weight:    2.9990
   chunk 89 optimal weight:    0.8980
   chunk 81 optimal weight:    0.8980
   chunk 9 optimal weight:   40.0000
   chunk 33 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 69 optimal weight:    6.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.133986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.103296 restraints weight = 25825.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.105946 restraints weight = 15905.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.107708 restraints weight = 11242.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.108633 restraints weight = 8838.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.109615 restraints weight = 7600.222|
|-----------------------------------------------------------------------------|
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7202
moved from start:          0.3253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8639  Z= 0.161
  Angle     :  0.631   8.566  11827  Z= 0.339
  Chirality :  0.041   0.321   1375
  Planarity :  0.004   0.059   1499
  Dihedral  :  4.061  18.888   1239
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 12.15
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.64 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  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:  1.83 (0.26), residues: 1153
  helix:  2.23 (0.17), residues: 864
  sheet:  None (None), residues: 0
  loop : -2.10 (0.38), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 465 
 TYR   0.014   0.001   TYR A 512 
 PHE   0.022   0.002   PHE A 394 
 TRP   0.060   0.002   TRP A 292 
 HIS   0.007   0.001   HIS A 616 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 8637)
  covalent geometry    : angle       0.63109 (11823)
  SS BOND              : bond        0.00357 (    2)
  SS BOND              : angle       1.09394 (    4)
  hydrogen bonds       : bond        0.03878 (  662)
  hydrogen bonds       : angle       3.86810 ( 1980)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1442.16 seconds
wall clock time: 25 minutes 42.37 seconds (1542.37 seconds total)