Starting phenix.real_space_refine
on Sat Jun  7 05:29:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yfu_39230/06_2025/8yfu_39230.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yfu_39230/06_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yfu_39230/06_2025/8yfu_39230.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yfu_39230/06_2025/8yfu_39230.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yfu_39230/06_2025/8yfu_39230.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yfu_39230/06_2025/8yfu_39230.cif"
  }
  resolution = 4.59
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.041
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 8419
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4222
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 583, 4222
          Classifications: {'peptide': 583}
          Incomplete info: {'truncation_to_alanine': 168}
          Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 562}
          Chain breaks: 1
          Unresolved chain link angles: 4
          Unresolved non-hydrogen bonds: 647
          Unresolved non-hydrogen angles: 817
          Unresolved non-hydrogen dihedrals: 541
          Unresolved non-hydrogen chiralities: 46
          Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 4, 'TYR:plan': 7, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 12, 'GLU:plan': 20, 'ARG:plan': 11}
          Unresolved non-hydrogen planarities: 391
    Chain: "B"
      Number of atoms: 4197
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 578, 4197
          Classifications: {'peptide': 578}
          Incomplete info: {'truncation_to_alanine': 164}
          Link IDs: {'PTRANS': 19, 'TRANS': 558}
          Chain breaks: 1
          Unresolved chain link angles: 4
          Unresolved non-hydrogen bonds: 624
          Unresolved non-hydrogen angles: 787
          Unresolved non-hydrogen dihedrals: 520
          Unresolved non-hydrogen chiralities: 46
          Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 11, 'GLU:plan': 19, 'ARG:plan': 11}
          Unresolved non-hydrogen planarities: 370
  Time building chain proxies: 5.58, per 1000 atoms: 0.66
  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: 2.65
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      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: 0.81
  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: 2.38

  Time building geometry restraints manager: 2.95 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:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     23.310
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.350
-------------------------------------------------------------------------------
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 : 12.72
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (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
 TRP   0.053   0.002   TRP A 395 
 HIS   0.010   0.001   HIS B 441 
 PHE   0.034   0.001   PHE A 517 
 TYR   0.017   0.001   TYR B 345 
 ARG   0.006   0.001   ARG A 604 

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

*********************** 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  : 1.280 
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: 0.1689
  time to fit residues: 45.8975
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  : 0.994 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    0.0980
   chunk 87 optimal weight:    0.7980
   chunk 48 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 58 optimal weight:   30.0000
   chunk 46 optimal weight:   10.0000
   chunk 90 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   chunk 54 optimal weight:    7.9990
   chunk 67 optimal weight:   50.0000
   chunk 104 optimal weight:    3.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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
B 387 HIS
B 619 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.139760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.109638 restraints weight = 26445.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.112497 restraints weight = 15437.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.114441 restraints weight = 10562.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7099
moved from start:          0.1014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8639  Z= 0.134
  Angle     :  0.581  12.277  11827  Z= 0.312
  Chirality :  0.038   0.256   1375
  Planarity :  0.004   0.055   1499
  Dihedral  :  3.823  19.265   1239
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.16 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  4.70 %
    Favored  : 95.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.91 (0.26), residues: 1153
  helix:  2.32 (0.17), residues: 861
  sheet:  None (None), residues: 0
  loop : -2.17 (0.39), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 395 
 HIS   0.007   0.001   HIS B 441 
 PHE   0.022   0.001   PHE A 517 
 TYR   0.023   0.001   TYR A 512 
 ARG   0.003   0.000   ARG B 604 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04227 (  662)
  hydrogen bonds       : angle       3.89880 ( 1980)
  SS BOND              : bond        0.00304 (    2)
  SS BOND              : angle       0.96527 (    4)
  covalent geometry    : bond        0.00252 ( 8637)
  covalent geometry    : angle       0.58128 (11823)

*********************** 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
  186 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 185
  time to evaluate  : 0.864 
Fit side-chains
   revert: symmetry clash
REVERT: A  284 LEU cc_start: 0.9187 (mt) cc_final: 0.8882 (mt)
REVERT: A  287 ILE cc_start: 0.9435 (mp) cc_final: 0.9200 (tp)
REVERT: A  413 MET cc_start: 0.8866 (ppp) cc_final: 0.8500 (ppp)
REVERT: A  508 MET cc_start: 0.6516 (mmt) cc_final: 0.5802 (mmp)
REVERT: A  558 TYR cc_start: 0.7989 (m-80) cc_final: 0.7751 (m-80)
REVERT: A  596 PHE cc_start: 0.7812 (m-80) cc_final: 0.7270 (m-10)
REVERT: A  600 GLU cc_start: 0.8584 (mp0) cc_final: 0.7953 (mm-30)
REVERT: B  241 CYS cc_start: 0.8693 (t) cc_final: 0.8391 (t)
REVERT: B  248 ASN cc_start: 0.9229 (t0) cc_final: 0.8901 (t0)
REVERT: B  280 GLU cc_start: 0.9161 (tt0) cc_final: 0.8560 (tp30)
REVERT: B  288 ASN cc_start: 0.9418 (m110) cc_final: 0.9146 (t0)
REVERT: B  398 ASP cc_start: 0.8812 (m-30) cc_final: 0.8612 (m-30)
REVERT: B  411 GLU cc_start: 0.9497 (tm-30) cc_final: 0.9154 (tm-30)
REVERT: B  462 GLN cc_start: 0.9120 (mp10) cc_final: 0.8881 (mp10)
REVERT: B  496 TYR cc_start: 0.8268 (t80) cc_final: 0.8023 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 185
  average time/residue: 0.1557
  time to fit residues: 42.2501
Evaluate side-chains
  153 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 62 optimal weight:   40.0000
   chunk 27 optimal weight:    0.0000
   chunk 65 optimal weight:    8.9990
   chunk 71 optimal weight:   40.0000
   chunk 91 optimal weight:    2.9990
   chunk 76 optimal weight:    8.9990
   chunk 87 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9990
   chunk 3 optimal weight:   20.0000
   chunk 38 optimal weight:   10.0000
   overall best weight:    2.7992

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

Flipped N/Q/H residues before XYZ refinement:
A 387 HIS
A 399 GLN
** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 614 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.133484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.099502 restraints weight = 26971.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.102038 restraints weight = 16884.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.103525 restraints weight = 12218.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7346
moved from start:          0.1938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.072   8639  Z= 0.248
  Angle     :  0.696  11.470  11827  Z= 0.379
  Chirality :  0.040   0.250   1375
  Planarity :  0.005   0.054   1499
  Dihedral  :  4.213  21.141   1239
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 14.75
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  5.20 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  7.12 %
    Favored  : 92.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.26), residues: 1153
  helix:  1.92 (0.17), residues: 856
  sheet:  None (None), residues: 0
  loop : -2.17 (0.38), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 395 
 HIS   0.007   0.002   HIS A 299 
 PHE   0.021   0.002   PHE A 386 
 TYR   0.018   0.002   TYR A 512 
 ARG   0.008   0.001   ARG B 459 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04726 (  662)
  hydrogen bonds       : angle       4.17543 ( 1980)
  SS BOND              : bond        0.04184 (    2)
  SS BOND              : angle       1.17485 (    4)
  covalent geometry    : bond        0.00508 ( 8637)
  covalent geometry    : angle       0.69557 (11823)

*********************** 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
  184 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 181
  time to evaluate  : 0.881 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  239 LEU cc_start: 0.8952 (tp) cc_final: 0.8681 (tp)
REVERT: A  280 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8413 (tm-30)
REVERT: A  413 MET cc_start: 0.8970 (ppp) cc_final: 0.8669 (ppp)
REVERT: A  508 MET cc_start: 0.7160 (mmt) cc_final: 0.6516 (mmm)
REVERT: A  558 TYR cc_start: 0.8073 (m-80) cc_final: 0.7719 (m-80)
REVERT: A  565 GLU cc_start: 0.9226 (tp30) cc_final: 0.8836 (tp30)
REVERT: A  604 ARG cc_start: 0.8099 (tpp80) cc_final: 0.7618 (tpp80)
REVERT: B  241 CYS cc_start: 0.8858 (t) cc_final: 0.8611 (t)
REVERT: B  248 ASN cc_start: 0.9250 (t0) cc_final: 0.8929 (t0)
REVERT: B  304 GLU cc_start: 0.8603 (pp20) cc_final: 0.8397 (pm20)
REVERT: B  411 GLU cc_start: 0.9468 (tm-30) cc_final: 0.9156 (tm-30)
REVERT: B  436 GLU cc_start: 0.8436 (tp30) cc_final: 0.8214 (pm20)
REVERT: B  509 VAL cc_start: 0.9239 (t) cc_final: 0.8958 (t)
REVERT: B  530 LEU cc_start: 0.9082 (mm) cc_final: 0.8878 (mm)
REVERT: B  605 PHE cc_start: 0.8449 (t80) cc_final: 0.8078 (t80)
  outliers start: 3
  outliers final: 0
  residues processed: 183
  average time/residue: 0.1410
  time to fit residues: 38.7153
Evaluate side-chains
  135 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 112 optimal weight:    0.0370
   chunk 46 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 70 optimal weight:   30.0000
   chunk 71 optimal weight:   20.0000
   chunk 114 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9980
   chunk 80 optimal weight:    1.9990
   chunk 88 optimal weight:    0.5980
   chunk 108 optimal weight:    3.9990
   overall best weight:    0.8660

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

Flipped N/Q/H residues before XYZ refinement:
B 387 HIS
B 504 HIS
B 555 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.136333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.105294 restraints weight = 25926.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.107964 restraints weight = 15694.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.109850 restraints weight = 11004.560|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7176
moved from start:          0.2066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8639  Z= 0.129
  Angle     :  0.586  11.028  11827  Z= 0.313
  Chirality :  0.038   0.243   1375
  Planarity :  0.004   0.058   1499
  Dihedral  :  3.961  19.426   1239
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.16 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.56 %
    Favored  : 96.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.90 (0.26), residues: 1153
  helix:  2.32 (0.17), residues: 859
  sheet:  None (None), residues: 0
  loop : -2.15 (0.38), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 292 
 HIS   0.006   0.001   HIS B 441 
 PHE   0.013   0.001   PHE B 605 
 TYR   0.013   0.001   TYR A 347 
 ARG   0.005   0.001   ARG A 270 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04002 (  662)
  hydrogen bonds       : angle       3.71548 ( 1980)
  SS BOND              : bond        0.00298 (    2)
  SS BOND              : angle       1.11427 (    4)
  covalent geometry    : bond        0.00263 ( 8637)
  covalent geometry    : angle       0.58603 (11823)

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

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 189
  time to evaluate  : 0.994 
Fit side-chains
   revert: symmetry clash
REVERT: A  273 ARG cc_start: 0.8884 (ptt180) cc_final: 0.8332 (ptt180)
REVERT: A  292 TRP cc_start: 0.8028 (m-10) cc_final: 0.7697 (m-10)
REVERT: A  413 MET cc_start: 0.9016 (ppp) cc_final: 0.8660 (ppp)
REVERT: A  508 MET cc_start: 0.6872 (mmt) cc_final: 0.5885 (mmp)
REVERT: A  558 TYR cc_start: 0.7995 (m-80) cc_final: 0.7617 (m-80)
REVERT: A  600 GLU cc_start: 0.8583 (mp0) cc_final: 0.8122 (mm-30)
REVERT: A  604 ARG cc_start: 0.7910 (tpp80) cc_final: 0.7519 (tpp80)
REVERT: B  241 CYS cc_start: 0.8885 (t) cc_final: 0.8654 (t)
REVERT: B  248 ASN cc_start: 0.9268 (t0) cc_final: 0.8923 (t0)
REVERT: B  280 GLU cc_start: 0.9139 (tt0) cc_final: 0.8601 (tp30)
REVERT: B  328 CYS cc_start: 0.8911 (m) cc_final: 0.8637 (m)
REVERT: B  411 GLU cc_start: 0.9482 (tm-30) cc_final: 0.9084 (tm-30)
REVERT: B  462 GLN cc_start: 0.9117 (mp10) cc_final: 0.8742 (mp10)
REVERT: B  509 VAL cc_start: 0.9233 (t) cc_final: 0.8972 (t)
REVERT: B  605 PHE cc_start: 0.8520 (t80) cc_final: 0.8244 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 189
  average time/residue: 0.1760
  time to fit residues: 48.9037
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  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 102 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 31 optimal weight:    4.9990
   chunk 73 optimal weight:   50.0000
   chunk 18 optimal weight:    0.0060
   chunk 50 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 109 optimal weight:    5.9990
   chunk 59 optimal weight:    2.9990
   chunk 72 optimal weight:    6.9990
   chunk 4 optimal weight:   30.0000
   overall best weight:    0.7398

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

Flipped N/Q/H residues before XYZ refinement:
B 387 HIS
B 504 HIS
B 555 GLN
B 608 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.137820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.104695 restraints weight = 25485.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.107219 restraints weight = 15967.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.108616 restraints weight = 11568.317|
|-----------------------------------------------------------------------------|
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7224
moved from start:          0.2285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8639  Z= 0.122
  Angle     :  0.575  10.349  11827  Z= 0.304
  Chirality :  0.038   0.235   1375
  Planarity :  0.003   0.056   1499
  Dihedral  :  3.862  19.193   1239
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.86 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.26), residues: 1153
  helix:  2.42 (0.17), residues: 864
  sheet:  None (None), residues: 0
  loop : -2.13 (0.38), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 395 
 HIS   0.006   0.001   HIS B 441 
 PHE   0.023   0.001   PHE A 235 
 TYR   0.012   0.001   TYR A 347 
 ARG   0.004   0.000   ARG A 270 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03691 (  662)
  hydrogen bonds       : angle       3.63654 ( 1980)
  SS BOND              : bond        0.00378 (    2)
  SS BOND              : angle       1.15575 (    4)
  covalent geometry    : bond        0.00248 ( 8637)
  covalent geometry    : angle       0.57423 (11823)

*********************** 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
  188 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.918 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  273 ARG cc_start: 0.8929 (ptt180) cc_final: 0.8504 (ptt90)
REVERT: A  280 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8182 (tm-30)
REVERT: A  413 MET cc_start: 0.8964 (ppp) cc_final: 0.8691 (ppp)
REVERT: A  508 MET cc_start: 0.6733 (mmt) cc_final: 0.5753 (mmp)
REVERT: A  558 TYR cc_start: 0.7672 (m-80) cc_final: 0.7287 (m-80)
REVERT: A  565 GLU cc_start: 0.9006 (tp30) cc_final: 0.8652 (tp30)
REVERT: A  566 ASP cc_start: 0.9450 (t0) cc_final: 0.9174 (t0)
REVERT: A  604 ARG cc_start: 0.7892 (tpp80) cc_final: 0.7479 (tpp80)
REVERT: B  241 CYS cc_start: 0.8853 (t) cc_final: 0.8585 (t)
REVERT: B  248 ASN cc_start: 0.9235 (t0) cc_final: 0.8877 (t0)
REVERT: B  280 GLU cc_start: 0.9152 (tt0) cc_final: 0.8572 (tp30)
REVERT: B  328 CYS cc_start: 0.8829 (m) cc_final: 0.8587 (m)
REVERT: B  408 MET cc_start: 0.9030 (pmm) cc_final: 0.8769 (pmm)
REVERT: B  411 GLU cc_start: 0.9465 (tm-30) cc_final: 0.9008 (tm-30)
REVERT: B  509 VAL cc_start: 0.9206 (t) cc_final: 0.8965 (t)
REVERT: B  605 PHE cc_start: 0.8488 (t80) cc_final: 0.8266 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 188
  average time/residue: 0.1726
  time to fit residues: 48.8128
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  : 1.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 6 optimal weight:   20.0000
   chunk 48 optimal weight:    0.9990
   chunk 91 optimal weight:    0.7980
   chunk 7 optimal weight:   40.0000
   chunk 40 optimal weight:    2.9990
   chunk 66 optimal weight:   40.0000
   chunk 8 optimal weight:   20.0000
   chunk 22 optimal weight:    3.9990
   chunk 105 optimal weight:    0.9990
   chunk 63 optimal weight:    8.9990
   chunk 106 optimal weight:    0.8980
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
B 504 HIS
B 555 GLN
B 614 ASN
B 618 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.134754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.104246 restraints weight = 25714.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.106865 restraints weight = 15636.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.108617 restraints weight = 11070.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7212
moved from start:          0.2503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8639  Z= 0.145
  Angle     :  0.578   9.472  11827  Z= 0.309
  Chirality :  0.038   0.156   1375
  Planarity :  0.004   0.065   1499
  Dihedral  :  3.957  22.591   1239
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.60 %
    Favored  : 95.14 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.03 (0.26), residues: 1153
  helix:  2.38 (0.17), residues: 867
  sheet:  None (None), residues: 0
  loop : -2.13 (0.38), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 292 
 HIS   0.006   0.001   HIS B 441 
 PHE   0.024   0.001   PHE B 358 
 TYR   0.014   0.001   TYR B 558 
 ARG   0.006   0.001   ARG B 459 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03714 (  662)
  hydrogen bonds       : angle       3.72903 ( 1980)
  SS BOND              : bond        0.00396 (    2)
  SS BOND              : angle       1.12664 (    4)
  covalent geometry    : bond        0.00304 ( 8637)
  covalent geometry    : angle       0.57782 (11823)

*********************** 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
  181 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 1.004 
Fit side-chains
   revert: symmetry clash
REVERT: A  251 LEU cc_start: 0.9318 (tp) cc_final: 0.9114 (tt)
REVERT: A  273 ARG cc_start: 0.9009 (ptt180) cc_final: 0.8572 (ptt90)
REVERT: A  413 MET cc_start: 0.9050 (ppp) cc_final: 0.8670 (ppp)
REVERT: A  482 LYS cc_start: 0.9428 (tttm) cc_final: 0.9222 (tptp)
REVERT: A  508 MET cc_start: 0.6826 (mmt) cc_final: 0.5768 (mmp)
REVERT: A  558 TYR cc_start: 0.7725 (m-80) cc_final: 0.7316 (m-80)
REVERT: A  565 GLU cc_start: 0.9100 (tp30) cc_final: 0.8709 (tp30)
REVERT: A  566 ASP cc_start: 0.9518 (t0) cc_final: 0.9172 (t0)
REVERT: A  600 GLU cc_start: 0.8410 (mp0) cc_final: 0.7690 (tp30)
REVERT: A  604 ARG cc_start: 0.8041 (tpp80) cc_final: 0.7283 (tpp80)
REVERT: B  241 CYS cc_start: 0.8823 (t) cc_final: 0.8573 (t)
REVERT: B  248 ASN cc_start: 0.9262 (t0) cc_final: 0.8907 (t0)
REVERT: B  280 GLU cc_start: 0.9195 (tt0) cc_final: 0.8680 (tp30)
REVERT: B  281 PHE cc_start: 0.8827 (t80) cc_final: 0.8581 (t80)
REVERT: B  328 CYS cc_start: 0.8865 (m) cc_final: 0.8641 (m)
REVERT: B  462 GLN cc_start: 0.9033 (mp10) cc_final: 0.8614 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 181
  average time/residue: 0.2243
  time to fit residues: 61.0617
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  : 1.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 62 optimal weight:   40.0000
   chunk 112 optimal weight:    0.9990
   chunk 77 optimal weight:    0.6980
   chunk 41 optimal weight:    0.7980
   chunk 71 optimal weight:   20.0000
   chunk 97 optimal weight:    0.0870
   chunk 18 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 70 optimal weight:    6.9990
   chunk 8 optimal weight:   20.0000
   chunk 87 optimal weight:    0.0050
   overall best weight:    0.5174

-------------------------------------------------------------------------------
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 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 504 HIS
B 555 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.137204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.106140 restraints weight = 25476.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.108784 restraints weight = 15717.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.110630 restraints weight = 11122.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.3801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7155
moved from start:          0.2628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8639  Z= 0.114
  Angle     :  0.562   8.785  11827  Z= 0.294
  Chirality :  0.038   0.140   1375
  Planarity :  0.004   0.083   1499
  Dihedral  :  3.845  19.717   1239
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.08 %
    Favored  : 95.66 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.18 (0.26), residues: 1153
  helix:  2.49 (0.17), residues: 865
  sheet:  None (None), residues: 0
  loop : -2.03 (0.38), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP A 395 
 HIS   0.006   0.001   HIS B 441 
 PHE   0.023   0.001   PHE A 235 
 TYR   0.027   0.001   TYR A 512 
 ARG   0.007   0.000   ARG B 465 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03453 (  662)
  hydrogen bonds       : angle       3.56082 ( 1980)
  SS BOND              : bond        0.00331 (    2)
  SS BOND              : angle       1.11036 (    4)
  covalent geometry    : bond        0.00229 ( 8637)
  covalent geometry    : angle       0.56159 (11823)

*********************** 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
  183 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 1.017 
Fit side-chains
REVERT: A  244 PHE cc_start: 0.9156 (t80) cc_final: 0.8923 (t80)
REVERT: A  273 ARG cc_start: 0.8969 (ptt180) cc_final: 0.8579 (ptt180)
REVERT: A  413 MET cc_start: 0.9088 (ppp) cc_final: 0.8707 (ppp)
REVERT: A  508 MET cc_start: 0.6666 (mmt) cc_final: 0.5881 (mmp)
REVERT: A  512 TYR cc_start: 0.8533 (m-80) cc_final: 0.8269 (m-10)
REVERT: A  558 TYR cc_start: 0.7652 (m-80) cc_final: 0.7276 (m-80)
REVERT: A  565 GLU cc_start: 0.9014 (tp30) cc_final: 0.8619 (tp30)
REVERT: A  566 ASP cc_start: 0.9498 (t0) cc_final: 0.9135 (t0)
REVERT: A  600 GLU cc_start: 0.8388 (mp0) cc_final: 0.7652 (tp30)
REVERT: A  604 ARG cc_start: 0.7996 (tpp80) cc_final: 0.7292 (tpp80)
REVERT: B  241 CYS cc_start: 0.8781 (t) cc_final: 0.8534 (t)
REVERT: B  248 ASN cc_start: 0.9278 (t0) cc_final: 0.8908 (t0)
REVERT: B  280 GLU cc_start: 0.9225 (tt0) cc_final: 0.8658 (tp30)
REVERT: B  328 CYS cc_start: 0.8890 (m) cc_final: 0.8625 (m)
REVERT: B  462 GLN cc_start: 0.9058 (mp10) cc_final: 0.8758 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 183
  average time/residue: 0.2071
  time to fit residues: 56.8166
Evaluate side-chains
  148 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 1.048 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 40 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9980
   chunk 94 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 55 optimal weight:    3.9990
   chunk 12 optimal weight:   30.0000
   chunk 71 optimal weight:   20.0000
   chunk 41 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 441 HIS
B 555 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.136441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.105946 restraints weight = 25870.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.108723 restraints weight = 15536.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.110692 restraints weight = 10778.038|
|-----------------------------------------------------------------------------|
r_work (final): 0.3790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7140
moved from start:          0.2776

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= 0.120
  Angle     :  0.590  13.222  11827  Z= 0.301
  Chirality :  0.037   0.187   1375
  Planarity :  0.004   0.060   1499
  Dihedral  :  3.829  18.267   1239
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.16 %
    Favored  : 95.58 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.15 (0.26), residues: 1153
  helix:  2.48 (0.17), residues: 864
  sheet:  None (None), residues: 0
  loop : -2.07 (0.38), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 395 
 HIS   0.013   0.001   HIS B 441 
 PHE   0.045   0.001   PHE B 605 
 TYR   0.020   0.001   TYR A 512 
 ARG   0.005   0.000   ARG B 465 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03425 (  662)
  hydrogen bonds       : angle       3.59783 ( 1980)
  SS BOND              : bond        0.00320 (    2)
  SS BOND              : angle       1.17589 (    4)
  covalent geometry    : bond        0.00249 ( 8637)
  covalent geometry    : angle       0.58955 (11823)

*********************** 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  : 1.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  244 PHE cc_start: 0.9137 (t80) cc_final: 0.8907 (t80)
REVERT: A  413 MET cc_start: 0.9106 (ppp) cc_final: 0.8717 (ppp)
REVERT: A  508 MET cc_start: 0.6932 (mmt) cc_final: 0.6276 (mmp)
REVERT: A  512 TYR cc_start: 0.8642 (m-80) cc_final: 0.8376 (m-10)
REVERT: A  558 TYR cc_start: 0.7628 (m-80) cc_final: 0.7192 (m-80)
REVERT: A  565 GLU cc_start: 0.8997 (tp30) cc_final: 0.8632 (tp30)
REVERT: A  566 ASP cc_start: 0.9413 (t0) cc_final: 0.9057 (t0)
REVERT: A  604 ARG cc_start: 0.8020 (tpp80) cc_final: 0.7341 (tpp80)
REVERT: B  241 CYS cc_start: 0.8832 (t) cc_final: 0.8560 (t)
REVERT: B  248 ASN cc_start: 0.9245 (t0) cc_final: 0.8912 (t0)
REVERT: B  280 GLU cc_start: 0.9216 (tt0) cc_final: 0.8579 (tp30)
REVERT: B  328 CYS cc_start: 0.8977 (m) cc_final: 0.8679 (m)
REVERT: B  395 TRP cc_start: 0.8654 (t60) cc_final: 0.8403 (t60)
REVERT: B  462 GLN cc_start: 0.9120 (mp10) cc_final: 0.8785 (mp10)
REVERT: B  509 VAL cc_start: 0.9297 (t) cc_final: 0.8964 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 186
  average time/residue: 0.2458
  time to fit residues: 68.5975
Evaluate side-chains
  154 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 1.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 103 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   chunk 63 optimal weight:    7.9990
   chunk 42 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 45 optimal weight:    0.6980
   chunk 69 optimal weight:    6.9990
   chunk 35 optimal weight:    0.0870
   chunk 90 optimal weight:    0.5980
   chunk 99 optimal weight:    0.9980
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
B 555 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.137370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.106926 restraints weight = 25873.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.109725 restraints weight = 15764.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.111219 restraints weight = 11018.440|
|-----------------------------------------------------------------------------|
r_work (final): 0.3805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7144
moved from start:          0.2813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046   8639  Z= 0.116
  Angle     :  0.574   9.116  11827  Z= 0.298
  Chirality :  0.037   0.182   1375
  Planarity :  0.004   0.059   1499
  Dihedral  :  3.802  17.982   1239
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.34 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.15 (0.26), residues: 1153
  helix:  2.47 (0.17), residues: 864
  sheet:  None (None), residues: 0
  loop : -2.05 (0.38), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 395 
 HIS   0.003   0.001   HIS B 441 
 PHE   0.023   0.001   PHE A 235 
 TYR   0.018   0.001   TYR A 512 
 ARG   0.004   0.000   ARG B 465 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03325 (  662)
  hydrogen bonds       : angle       3.56463 ( 1980)
  SS BOND              : bond        0.00311 (    2)
  SS BOND              : angle       1.10103 (    4)
  covalent geometry    : bond        0.00242 ( 8637)
  covalent geometry    : angle       0.57395 (11823)

*********************** 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
  183 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 0.978 
Fit side-chains
REVERT: A  244 PHE cc_start: 0.9153 (t80) cc_final: 0.8896 (t80)
REVERT: A  273 ARG cc_start: 0.8969 (ptt180) cc_final: 0.8494 (ptt90)
REVERT: A  399 GLN cc_start: 0.8436 (mm110) cc_final: 0.8084 (mm-40)
REVERT: A  413 MET cc_start: 0.9100 (ppp) cc_final: 0.8733 (ppp)
REVERT: A  508 MET cc_start: 0.6935 (mmt) cc_final: 0.6176 (mmp)
REVERT: A  512 TYR cc_start: 0.8624 (m-80) cc_final: 0.8326 (m-10)
REVERT: A  558 TYR cc_start: 0.7590 (m-80) cc_final: 0.7198 (m-80)
REVERT: A  565 GLU cc_start: 0.8981 (tp30) cc_final: 0.8625 (tp30)
REVERT: A  566 ASP cc_start: 0.9387 (t0) cc_final: 0.9013 (t0)
REVERT: A  604 ARG cc_start: 0.7978 (tpp80) cc_final: 0.7050 (tpp80)
REVERT: B  241 CYS cc_start: 0.8782 (t) cc_final: 0.8536 (t)
REVERT: B  248 ASN cc_start: 0.9245 (t0) cc_final: 0.8867 (t0)
REVERT: B  280 GLU cc_start: 0.9236 (tt0) cc_final: 0.8678 (tp30)
REVERT: B  328 CYS cc_start: 0.8863 (m) cc_final: 0.8593 (m)
REVERT: B  398 ASP cc_start: 0.8877 (m-30) cc_final: 0.8652 (m-30)
REVERT: B  462 GLN cc_start: 0.9101 (mp10) cc_final: 0.8767 (mp10)
REVERT: B  509 VAL cc_start: 0.9259 (t) cc_final: 0.8924 (t)
REVERT: B  524 TYR cc_start: 0.7282 (t80) cc_final: 0.6986 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 183
  average time/residue: 0.1474
  time to fit residues: 40.5726
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  : 0.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 65 optimal weight:   30.0000
   chunk 101 optimal weight:    0.9990
   chunk 27 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 97 optimal weight:    0.0040
   chunk 73 optimal weight:   50.0000
   chunk 24 optimal weight:    0.8980
   chunk 7 optimal weight:   20.0000
   chunk 1 optimal weight:   40.0000
   overall best weight:    0.6392

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

Flipped N/Q/H residues before XYZ refinement:
B 298 ASN
B 555 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.138891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.105929 restraints weight = 25731.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.108644 restraints weight = 15947.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.109997 restraints weight = 11354.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7192
moved from start:          0.2933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   8639  Z= 0.117
  Angle     :  0.593  14.837  11827  Z= 0.304
  Chirality :  0.038   0.184   1375
  Planarity :  0.004   0.060   1499
  Dihedral  :  3.777  17.475   1239
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.51 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.13 (0.26), residues: 1153
  helix:  2.45 (0.17), residues: 864
  sheet:  None (None), residues: 0
  loop : -2.03 (0.38), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP A 395 
 HIS   0.003   0.001   HIS B 441 
 PHE   0.023   0.001   PHE A 235 
 TYR   0.019   0.001   TYR A 512 
 ARG   0.004   0.000   ARG B 459 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03308 (  662)
  hydrogen bonds       : angle       3.56829 ( 1980)
  SS BOND              : bond        0.00312 (    2)
  SS BOND              : angle       1.06023 (    4)
  covalent geometry    : bond        0.00245 ( 8637)
  covalent geometry    : angle       0.59317 (11823)

********************** 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
  184 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.958 
Fit side-chains
REVERT: A  244 PHE cc_start: 0.9175 (t80) cc_final: 0.8931 (t80)
REVERT: A  273 ARG cc_start: 0.8979 (ptt180) cc_final: 0.8330 (ptt90)
REVERT: A  413 MET cc_start: 0.9028 (ppp) cc_final: 0.8687 (ppp)
REVERT: A  489 MET cc_start: 0.8866 (tpp) cc_final: 0.8624 (tpt)
REVERT: A  508 MET cc_start: 0.6784 (mmt) cc_final: 0.6093 (mmp)
REVERT: A  512 TYR cc_start: 0.8654 (m-80) cc_final: 0.8348 (m-10)
REVERT: A  558 TYR cc_start: 0.7572 (m-80) cc_final: 0.7169 (m-80)
REVERT: A  565 GLU cc_start: 0.8957 (tp30) cc_final: 0.8610 (tp30)
REVERT: A  566 ASP cc_start: 0.9380 (t0) cc_final: 0.9011 (t0)
REVERT: A  604 ARG cc_start: 0.8086 (tpp80) cc_final: 0.7104 (tpp80)
REVERT: B  241 CYS cc_start: 0.8766 (t) cc_final: 0.8531 (t)
REVERT: B  248 ASN cc_start: 0.9221 (t0) cc_final: 0.8913 (t0)
REVERT: B  280 GLU cc_start: 0.9220 (tt0) cc_final: 0.8622 (tp30)
REVERT: B  328 CYS cc_start: 0.8842 (m) cc_final: 0.8611 (m)
REVERT: B  377 LEU cc_start: 0.8625 (mm) cc_final: 0.8201 (mm)
REVERT: B  509 VAL cc_start: 0.9225 (t) cc_final: 0.8892 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 184
  average time/residue: 0.1543
  time to fit residues: 42.6246
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  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 48 optimal weight:    0.8980
   chunk 108 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 76 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0570
   chunk 55 optimal weight:    0.5980
   chunk 5 optimal weight:   40.0000
   chunk 19 optimal weight:    8.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.8300

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

Flipped N/Q/H residues before XYZ refinement:
B 555 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.136937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.106845 restraints weight = 25808.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.109617 restraints weight = 15697.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.111491 restraints weight = 10921.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7145
moved from start:          0.2997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8639  Z= 0.120
  Angle     :  0.579   9.570  11827  Z= 0.304
  Chirality :  0.038   0.180   1375
  Planarity :  0.004   0.060   1499
  Dihedral  :  3.757  17.409   1239
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.51 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.16 (0.26), residues: 1153
  helix:  2.47 (0.17), residues: 864
  sheet:  None (None), residues: 0
  loop : -2.02 (0.38), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A 395 
 HIS   0.003   0.001   HIS B 441 
 PHE   0.023   0.001   PHE A 235 
 TYR   0.016   0.001   TYR A 512 
 ARG   0.004   0.000   ARG B 459 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03292 (  662)
  hydrogen bonds       : angle       3.57806 ( 1980)
  SS BOND              : bond        0.00328 (    2)
  SS BOND              : angle       1.04817 (    4)
  covalent geometry    : bond        0.00255 ( 8637)
  covalent geometry    : angle       0.57899 (11823)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2951.86 seconds
wall clock time: 54 minutes 12.46 seconds (3252.46 seconds total)