Starting phenix.real_space_refine
on Wed Feb  4 07:02:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yr3_39534/02_2026/8yr3_39534.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yr3_39534/02_2026/8yr3_39534.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yr3_39534/02_2026/8yr3_39534.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yr3_39534/02_2026/8yr3_39534.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yr3_39534/02_2026/8yr3_39534.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yr3_39534/02_2026/8yr3_39534.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.016
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: 5
    Type Number    sf(0)   Gaussians
     Cd      1      9.23       5
     S      36      5.16       5
     C    5978      2.51       5
     N    1616      2.21       5
     O    1688      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9319
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4639
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 587, 4639
          Classifications: {'peptide': 587}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 13, 'TRANS': 573}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "B"
      Number of atoms: 4639
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 587, 4639
          Classifications: {'peptide': 587}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 13, 'TRANS': 573}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "A"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 20
          Ad-hoc single atom residues: {' CD': 1}
          Unusual residues: {'GSH': 1}
          Classifications: {'undetermined': 1}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 20
          Unusual residues: {'GSH': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.17, per 1000 atoms: 0.23
  Number of scatterers: 9319
  At special positions: 0
  Unit cell: (72.21, 101.26, 138.61, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cd      1     47.96
     S      36     16.00
     O    1688      8.00
     N    1616      7.00
     C    5978      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.52
  Conformation dependent library (CDL) restraints added in 230.6 milliseconds
  

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2160

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 5 sheets defined
      71.0% alpha, 5.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.48
  Creating SS restraints...
    Processing helix  chain 'A' and resid 241 through 254
      removed outlier: 4.187A  pdb=" N   LYS A 245 " --> pdb=" O   ASP A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 295
      Proline residue:  A 283  - end of helix
    Processing helix  chain 'A' and resid 298 through 316
    Processing helix  chain 'A' and resid 324 through 355
      removed outlier: 4.583A  pdb=" N   ARG A 336 " --> pdb=" O   PHE A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 364
      removed outlier: 3.956A  pdb=" N   HIS A 361 " --> pdb=" O   SER A 357 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ARG A 364 " --> pdb=" O   TRP A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 391
      removed outlier: 3.715A  pdb=" N   VAL A 369 " --> pdb=" O   ARG A 365 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   LEU A 384 " --> pdb=" O   VAL A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 409
      removed outlier: 3.619A  pdb=" N   PHE A 409 " --> pdb=" O   PHE A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 455
      removed outlier: 3.702A  pdb=" N   VAL A 454 " --> pdb=" O   ARG A 450 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ASP A 455 " --> pdb=" O   ALA A 451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 466
    Processing helix  chain 'A' and resid 468 through 522
      removed outlier: 3.726A  pdb=" N   GLU A 522 " --> pdb=" O   TYR A 518 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 570
      removed outlier: 4.203A  pdb=" N   VAL A 531 " --> pdb=" O   VAL A 527 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ILE A 538 " --> pdb=" O   GLY A 534 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   GLN A 539 " --> pdb=" O   THR A 535 " (cutoff:3.500A)
      Proline residue:  A 543  - end of helix
      removed outlier: 3.737A  pdb=" N   TYR A 551 " --> pdb=" O   PHE A 547 " (cutoff:3.500A)
      removed outlier: 4.845A  pdb=" N   ARG A 552 " --> pdb=" O   GLY A 548 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   MET A 553 " --> pdb=" O   THR A 549 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 636
    Processing helix  chain 'A' and resid 655 through 657
      No H-bonds generated for 'chain 'A' and resid 655 through 657'
    Processing helix  chain 'A' and resid 658 through 665
      removed outlier: 3.757A  pdb=" N   LEU A 662 " --> pdb=" O   THR A 658 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 679 through 686
    Processing helix  chain 'A' and resid 692 through 703
      removed outlier: 3.752A  pdb=" N   VAL A 696 " --> pdb=" O   GLY A 692 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 705 through 712
    Processing helix  chain 'A' and resid 714 through 718
    Processing helix  chain 'A' and resid 728 through 744
    Processing helix  chain 'A' and resid 758 through 774
    Processing helix  chain 'A' and resid 785 through 790
      removed outlier: 4.643A  pdb=" N   ASN A 790 " --> pdb=" O   SER A 786 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 807 through 815
      removed outlier: 4.259A  pdb=" N   GLY A 815 " --> pdb=" O   LEU A 811 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 817 through 826
      removed outlier: 3.765A  pdb=" N   GLN A 826 " --> pdb=" O   TRP A 822 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 254
      removed outlier: 3.879A  pdb=" N   LYS B 245 " --> pdb=" O   ASP B 241 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 261 through 295
      removed outlier: 3.586A  pdb=" N   VAL B 280 " --> pdb=" O   ARG B 276 " (cutoff:3.500A)
      Proline residue:  B 283  - end of helix
    Processing helix  chain 'B' and resid 298 through 316
    Processing helix  chain 'B' and resid 324 through 355
      removed outlier: 4.588A  pdb=" N   ARG B 336 " --> pdb=" O   PHE B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 357 through 364
      removed outlier: 3.862A  pdb=" N   HIS B 361 " --> pdb=" O   SER B 357 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ARG B 364 " --> pdb=" O   TRP B 360 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 365 through 391
      removed outlier: 3.730A  pdb=" N   VAL B 369 " --> pdb=" O   ARG B 365 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   LEU B 384 " --> pdb=" O   VAL B 380 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 391 through 409
      removed outlier: 3.576A  pdb=" N   PHE B 409 " --> pdb=" O   PHE B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 455
      removed outlier: 4.173A  pdb=" N   LEU B 415 " --> pdb=" O   ALA B 411 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   MET B 442 " --> pdb=" O   PHE B 438 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   ASP B 455 " --> pdb=" O   ALA B 451 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 461 through 466
    Processing helix  chain 'B' and resid 468 through 522
      removed outlier: 3.736A  pdb=" N   GLY B 506 " --> pdb=" O   ASN B 502 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   GLU B 522 " --> pdb=" O   TYR B 518 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 526 through 542
      removed outlier: 4.329A  pdb=" N   TYR B 530 " --> pdb=" O   GLN B 526 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   VAL B 531 " --> pdb=" O   VAL B 527 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 543 through 545
      No H-bonds generated for 'chain 'B' and resid 543 through 545'
    Processing helix  chain 'B' and resid 546 through 570
      removed outlier: 3.502A  pdb=" N   PHE B 558 " --> pdb=" O   ILE B 554 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 627 through 636
    Processing helix  chain 'B' and resid 655 through 657
      No H-bonds generated for 'chain 'B' and resid 655 through 657'
    Processing helix  chain 'B' and resid 658 through 665
      removed outlier: 3.932A  pdb=" N   LEU B 662 " --> pdb=" O   THR B 658 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 679 through 686
    Processing helix  chain 'B' and resid 692 through 703
      removed outlier: 3.845A  pdb=" N   VAL B 696 " --> pdb=" O   GLY B 692 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 705 through 712
      removed outlier: 3.737A  pdb=" N   PHE B 712 " --> pdb=" O   ALA B 708 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 714 through 718
      removed outlier: 3.837A  pdb=" N   ARG B 717 " --> pdb=" O   GLU B 714 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 728 through 744
    Processing helix  chain 'B' and resid 758 through 774
    Processing helix  chain 'B' and resid 785 through 790
      removed outlier: 4.701A  pdb=" N   ASN B 790 " --> pdb=" O   SER B 786 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 807 through 815
      removed outlier: 3.505A  pdb=" N   LEU B 811 " --> pdb=" O   ARG B 807 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   GLY B 815 " --> pdb=" O   LEU B 811 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 817 through 826
      removed outlier: 3.773A  pdb=" N   GLN B 826 " --> pdb=" O   TRP B 822 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 606 through 609
      removed outlier: 5.446A  pdb=" N   VAL A 595 " --> pdb=" O   ASP A 608 " (cutoff:3.500A)
      removed outlier: 4.458A  pdb=" N   ILE A 590 " --> pdb=" O   VAL A 613 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   VAL A 613 " --> pdb=" O   ILE A 590 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 606 through 609
      removed outlier: 5.446A  pdb=" N   VAL A 595 " --> pdb=" O   ASP A 608 " (cutoff:3.500A)
      removed outlier: 5.674A  pdb=" N   PHE A 592 " --> pdb=" O   ARG A 648 " (cutoff:3.500A)
      removed outlier: 7.891A  pdb=" N   ARG A 648 " --> pdb=" O   PHE A 592 " (cutoff:3.500A)
      removed outlier: 5.643A  pdb=" N   ASN A 594 " --> pdb=" O   CYS A 646 " (cutoff:3.500A)
      removed outlier: 5.180A  pdb=" N   CYS A 646 " --> pdb=" O   ASN A 594 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 666 through 667
      removed outlier: 6.187A  pdb=" N   LEU A 619 " --> pdb=" O   VAL A 780 " (cutoff:3.500A)
      removed outlier: 7.969A  pdb=" N   LEU A 795 " --> pdb=" O   THR A 618 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   ALA A 620 " --> pdb=" O   LEU A 795 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 606 through 609
      removed outlier: 5.273A  pdb=" N   VAL B 595 " --> pdb=" O   ASP B 608 " (cutoff:3.500A)
      removed outlier: 5.562A  pdb=" N   PHE B 592 " --> pdb=" O   ARG B 648 " (cutoff:3.500A)
      removed outlier: 7.473A  pdb=" N   ARG B 648 " --> pdb=" O   PHE B 592 " (cutoff:3.500A)
      removed outlier: 5.902A  pdb=" N   ASN B 594 " --> pdb=" O   CYS B 646 " (cutoff:3.500A)
      removed outlier: 5.487A  pdb=" N   CYS B 646 " --> pdb=" O   ASN B 594 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 666 through 667
      removed outlier: 6.316A  pdb=" N   ILE B 748 " --> pdb=" O   ILE B 779 " (cutoff:3.500A)
      removed outlier: 7.712A  pdb=" N   VAL B 781 " --> pdb=" O   ILE B 748 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   LEU B 619 " --> pdb=" O   VAL B 780 " (cutoff:3.500A)

    616 hydrogen bonds defined for protein.
    1818 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.29

  Time building geometry restraints manager: 0.71 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1505
        1.30 -     1.43: 2531
        1.43 -     1.56: 5400
        1.56 -     1.69: 2
        1.69 -     1.82: 58
  Bond restraints: 9496
  Sorted by residual:
  bond pdb=" C   MET A 542 "
       pdb=" O   MET A 542 "
    ideal  model  delta    sigma   weight residual
    1.238  1.398 -0.160 1.28e-02 6.10e+03 1.57e+02
  bond pdb=" C   GLN A 539 "
       pdb=" O   GLN A 539 "
    ideal  model  delta    sigma   weight residual
    1.236  1.369 -0.132 1.15e-02 7.56e+03 1.32e+02
  bond pdb=" C   ASN A 545 "
       pdb=" O   ASN A 545 "
    ideal  model  delta    sigma   weight residual
    1.236  1.355 -0.119 1.15e-02 7.56e+03 1.06e+02
  bond pdb=" CA  PHE A 547 "
       pdb=" C   PHE A 547 "
    ideal  model  delta    sigma   weight residual
    1.524  1.414  0.110 1.24e-02 6.50e+03 7.83e+01
  bond pdb=" N   THR A 549 "
       pdb=" CA  THR A 549 "
    ideal  model  delta    sigma   weight residual
    1.459  1.543 -0.084 1.16e-02 7.43e+03 5.27e+01
  ... (remaining 9491 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.15: 12713
        4.15 -     8.29: 137
        8.29 -    12.44: 21
       12.44 -    16.59: 1
       16.59 -    20.74: 2
  Bond angle restraints: 12874
  Sorted by residual:
  angle pdb=" C   MET A 542 "
        pdb=" N   PRO A 543 "
        pdb=" CA  PRO A 543 "
      ideal   model   delta    sigma   weight residual
     119.05   98.74   20.31 1.11e+00 8.12e-01 3.35e+02
  angle pdb=" C   ASN A 545 "
        pdb=" N   TRP A 546 "
        pdb=" CA  TRP A 546 "
      ideal   model   delta    sigma   weight residual
     120.99  100.25   20.74 1.86e+00 2.89e-01 1.24e+02
  angle pdb=" N   LEU B 507 "
        pdb=" CA  LEU B 507 "
        pdb=" C   LEU B 507 "
      ideal   model   delta    sigma   weight residual
     111.33   99.40   11.93 1.21e+00 6.83e-01 9.72e+01
  angle pdb=" CA  ASN A 545 "
        pdb=" C   ASN A 545 "
        pdb=" O   ASN A 545 "
      ideal   model   delta    sigma   weight residual
     121.00  130.26   -9.26 1.05e+00 9.07e-01 7.77e+01
  angle pdb=" N   SER B 493 "
        pdb=" CA  SER B 493 "
        pdb=" C   SER B 493 "
      ideal   model   delta    sigma   weight residual
     111.82  102.11    9.71 1.16e+00 7.43e-01 7.00e+01
  ... (remaining 12869 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.30: 4708
       17.30 -    34.60: 667
       34.60 -    51.90: 195
       51.90 -    69.20: 32
       69.20 -    86.50: 14
  Dihedral angle restraints: 5616
    sinusoidal: 2242
      harmonic: 3374
  Sorted by residual:
  dihedral pdb=" N   THR A 549 "
           pdb=" C   THR A 549 "
           pdb=" CA  THR A 549 "
           pdb=" CB  THR A 549 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  133.20   -9.80     0      2.50e+00 1.60e-01 1.54e+01
  dihedral pdb=" C   PHE A 547 "
           pdb=" N   PHE A 547 "
           pdb=" CA  PHE A 547 "
           pdb=" CB  PHE A 547 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.61   -8.99     0      2.50e+00 1.60e-01 1.29e+01
  dihedral pdb=" CA  LYS A 575 "
           pdb=" C   LYS A 575 "
           pdb=" N   ASP A 576 "
           pdb=" CA  ASP A 576 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.36  -17.64     0      5.00e+00 4.00e-02 1.24e+01
  ... (remaining 5613 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 1234
       0.061 -    0.123: 207
       0.123 -    0.184: 31
       0.184 -    0.245: 10
       0.245 -    0.307: 4
  Chirality restraints: 1486
  Sorted by residual:
  chirality pdb=" CG  LEU A 635 "
            pdb=" CB  LEU A 635 "
            pdb=" CD1 LEU A 635 "
            pdb=" CD2 LEU A 635 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.28   -0.31 2.00e-01 2.50e+01 2.35e+00
  chirality pdb=" CA  MET A 553 "
            pdb=" N   MET A 553 "
            pdb=" C   MET A 553 "
            pdb=" CB  MET A 553 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.98e+00
  chirality pdb=" CA  THR B 432 "
            pdb=" N   THR B 432 "
            pdb=" C   THR B 432 "
            pdb=" CB  THR B 432 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.26    0.27 2.00e-01 2.50e+01 1.82e+00
  ... (remaining 1483 not shown)

  Planarity restraints: 1632
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  GSH B 901 "    0.082 2.00e-02 2.50e+03   2.47e-01 7.63e+02
        pdb=" CA2 GSH B 901 "   -0.193 2.00e-02 2.50e+03
        pdb=" CA3 GSH B 901 "   -0.297 2.00e-02 2.50e+03
        pdb=" N3  GSH B 901 "    0.416 2.00e-02 2.50e+03
        pdb=" O2  GSH B 901 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  GSH A 901 "   -0.068 2.00e-02 2.50e+03   2.01e-01 5.04e+02
        pdb=" CA2 GSH A 901 "    0.172 2.00e-02 2.50e+03
        pdb=" CA3 GSH A 901 "    0.243 2.00e-02 2.50e+03
        pdb=" N3  GSH A 901 "   -0.329 2.00e-02 2.50e+03
        pdb=" O2  GSH A 901 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG1 GSH B 901 "    0.175 2.00e-02 2.50e+03   1.99e-01 4.93e+02
        pdb=" CD1 GSH B 901 "   -0.075 2.00e-02 2.50e+03
        pdb=" OE1 GSH B 901 "   -0.027 2.00e-02 2.50e+03
        pdb=" CA2 GSH B 901 "    0.244 2.00e-02 2.50e+03
        pdb=" N2  GSH B 901 "   -0.317 2.00e-02 2.50e+03
  ... (remaining 1629 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 2008
        2.77 -     3.30: 9242
        3.30 -     3.83: 15198
        3.83 -     4.37: 15843
        4.37 -     4.90: 27608
  Nonbonded interactions: 69899
  Sorted by model distance:
  nonbonded pdb=" O   THR A 428 "
            pdb=" OG1 THR A 432 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" OD1 ASP A 678 "
            pdb=" N   THR A 679 "
     model   vdw
     2.240 3.120
  nonbonded pdb=" O   THR B 320 "
            pdb=" OG1 THR B 320 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" ND2 ASN A 279 "
            pdb=" OD2 ASP A 397 "
     model   vdw
     2.255 3.120
  nonbonded pdb=" NZ  LYS B 245 "
            pdb=" OE1 GLU B 562 "
     model   vdw
     2.258 3.120
  ... (remaining 69894 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 240 through 901)
  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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             2.060
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.090
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8547
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      :  0.008   0.160   9496  Z= 0.583
  Angle     :  1.029  20.736  12874  Z= 0.653
  Chirality :  0.051   0.307   1486
  Planarity :  0.011   0.247   1632
  Dihedral  : 17.688  86.505   3456
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 15.64
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  6.67 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 29.29 %
    Favored  : 69.39 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.25 (0.25), residues: 1170
  helix:  1.26 (0.19), residues: 756
  sheet:  1.01 (0.68), residues: 60
  loop : -2.47 (0.29), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 552 
 TYR   0.020   0.002   TYR A 550 
 PHE   0.021   0.002   PHE A 585 
 TRP   0.042   0.003   TRP A 822 
 HIS   0.004   0.001   HIS A 596 

Details of bonding type rmsd
  covalent geometry    : bond        0.00834 ( 9496)
  covalent geometry    : angle       1.02921 (12874)
  hydrogen bonds       : bond        0.14745 (  613)
  hydrogen bonds       : angle       6.03120 ( 1818)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 144
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  416 ILE cc_start: 0.9160 (mm) cc_final: 0.8940 (mm)
REVERT: A  542 MET cc_start: 0.9405 (OUTLIER) cc_final: 0.9097 (mpp)
REVERT: A  543 PRO cc_start: 0.9162 (OUTLIER) cc_final: 0.8945 (Cg_exo)
REVERT: A  566 ASP cc_start: 0.9598 (t0) cc_final: 0.9368 (t0)
REVERT: A  706 HIS cc_start: 0.9105 (t70) cc_final: 0.8094 (t70)
REVERT: B  330 ARG cc_start: 0.9036 (tmm160) cc_final: 0.8782 (ttp80)
REVERT: B  416 ILE cc_start: 0.9143 (mm) cc_final: 0.8922 (mm)
REVERT: B  455 ASP cc_start: 0.9281 (m-30) cc_final: 0.8736 (p0)
REVERT: B  566 ASP cc_start: 0.9511 (t0) cc_final: 0.9192 (t0)
REVERT: B  586 GLN cc_start: 0.7983 (mm110) cc_final: 0.7496 (mm110)
REVERT: B  668 VAL cc_start: 0.9565 (t) cc_final: 0.9255 (m)
REVERT: B  710 MET cc_start: 0.9308 (mmt) cc_final: 0.9027 (mpp)
REVERT: B  749 LEU cc_start: 0.9532 (mm) cc_final: 0.9258 (mm)
  outliers start: 13
  outliers final: 7
  residues processed: 156
  average time/residue: 0.0796
  time to fit residues: 17.7511
Evaluate side-chains
  103 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  436 THR
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  542 MET
Chi-restraints excluded: chain A residue  543 PRO
Chi-restraints excluded: chain A residue  549 THR
Chi-restraints excluded: chain B residue  436 THR
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain B residue  505 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 49 optimal weight:    0.3980
   chunk 97 optimal weight:    6.9990
   chunk 113 optimal weight:    7.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.0470
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:   10.0000
   overall best weight:    1.4482

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

Flipped N/Q/H residues before XYZ refinement:
A 501 GLN
A 719 GLN
A 733 GLN
** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 719 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.082420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.059654 restraints weight = 36565.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 5.32
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3145
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3145 r_free = 0.3145    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3144 r_free = 0.3144    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3144
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8502
moved from start:          0.1679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9496  Z= 0.155
  Angle     :  0.633  10.628  12874  Z= 0.328
  Chirality :  0.042   0.265   1486
  Planarity :  0.004   0.036   1632
  Dihedral  :  6.290  50.994   1348
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 27.47 %
    Favored  : 68.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.24), residues: 1170
  helix:  1.80 (0.19), residues: 750
  sheet:  0.90 (0.64), residues: 62
  loop : -2.25 (0.28), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 365 
 TYR   0.017   0.001   TYR A 550 
 PHE   0.013   0.001   PHE A 325 
 TRP   0.038   0.002   TRP A 434 
 HIS   0.005   0.001   HIS A 808 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 9496)
  covalent geometry    : angle       0.63276 (12874)
  hydrogen bonds       : bond        0.07074 (  613)
  hydrogen bonds       : angle       4.34970 ( 1818)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 105
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  428 THR cc_start: 0.9544 (OUTLIER) cc_final: 0.9323 (p)
REVERT: A  458 LEU cc_start: 0.9580 (tp) cc_final: 0.9376 (tt)
REVERT: B  374 ASP cc_start: 0.9227 (m-30) cc_final: 0.8943 (t0)
REVERT: B  455 ASP cc_start: 0.9163 (m-30) cc_final: 0.8639 (p0)
REVERT: B  562 GLU cc_start: 0.9552 (tp30) cc_final: 0.9140 (mm-30)
REVERT: B  566 ASP cc_start: 0.9647 (t0) cc_final: 0.9419 (t0)
REVERT: B  749 LEU cc_start: 0.9610 (mm) cc_final: 0.9312 (mm)
  outliers start: 44
  outliers final: 18
  residues processed: 144
  average time/residue: 0.0652
  time to fit residues: 14.7425
Evaluate side-chains
  109 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  366 THR
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  403 ILE
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain A residue  630 SER
Chi-restraints excluded: chain A residue  654 ILE
Chi-restraints excluded: chain A residue  676 PHE
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  258 SER
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  436 THR
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  505 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 100 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 64 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 68 optimal weight:    5.9990
   chunk 74 optimal weight:    6.9990
   chunk 46 optimal weight:    7.9990
   chunk 3 optimal weight:    6.9990
   chunk 99 optimal weight:   10.0000
   chunk 16 optimal weight:    0.4980
   chunk 11 optimal weight:    4.9990
   overall best weight:    3.0986

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

Flipped N/Q/H residues before XYZ refinement:
B 677 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.082796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.058312 restraints weight = 39026.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.3077 rms_B_bonded: 5.37
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3076
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3076 r_free = 0.3076    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3076 r_free = 0.3076    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3076
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8614
moved from start:          0.2332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9496  Z= 0.205
  Angle     :  0.623  10.891  12874  Z= 0.330
  Chirality :  0.041   0.291   1486
  Planarity :  0.004   0.044   1632
  Dihedral  :  5.675  48.488   1338
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 28.59 %
    Favored  : 67.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.09 (0.24), residues: 1170
  helix:  1.96 (0.19), residues: 756
  sheet:  0.62 (0.62), residues: 62
  loop : -2.16 (0.29), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 364 
 TYR   0.015   0.002   TYR B 536 
 PHE   0.012   0.001   PHE A 325 
 TRP   0.044   0.002   TRP A 822 
 HIS   0.004   0.001   HIS B 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 9496)
  covalent geometry    : angle       0.62293 (12874)
  hydrogen bonds       : bond        0.07044 (  613)
  hydrogen bonds       : angle       4.40734 ( 1818)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 92
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  312 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9328 (mp)
REVERT: B  455 ASP cc_start: 0.9219 (m-30) cc_final: 0.8737 (p0)
REVERT: B  562 GLU cc_start: 0.9512 (tp30) cc_final: 0.9057 (mm-30)
REVERT: B  566 ASP cc_start: 0.9666 (t0) cc_final: 0.9448 (t0)
  outliers start: 36
  outliers final: 22
  residues processed: 122
  average time/residue: 0.0750
  time to fit residues: 14.2883
Evaluate side-chains
  108 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 85
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  354 HIS
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  444 THR
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain A residue  630 SER
Chi-restraints excluded: chain A residue  654 ILE
Chi-restraints excluded: chain A residue  676 PHE
Chi-restraints excluded: chain A residue  739 ARG
Chi-restraints excluded: chain A residue  750 LEU
Chi-restraints excluded: chain A residue  754 THR
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  258 SER
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  422 SER
Chi-restraints excluded: chain B residue  505 ILE
Chi-restraints excluded: chain B residue  614 MET
Chi-restraints excluded: chain B residue  811 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9980
   chunk 24 optimal weight:    4.9990
   chunk 43 optimal weight:    9.9990
   chunk 28 optimal weight:    0.0020
   chunk 41 optimal weight:    2.9990
   chunk 93 optimal weight:    6.9990
   chunk 65 optimal weight:    4.9990
   chunk 70 optimal weight:    9.9990
   chunk 34 optimal weight:    9.9990
   overall best weight:    1.9994

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

Flipped N/Q/H residues before XYZ refinement:
A 652 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.085639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.061288 restraints weight = 41705.259|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 5.58
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3043
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3043 r_free = 0.3043    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3043 r_free = 0.3043    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3043
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8572
moved from start:          0.2715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9496  Z= 0.158
  Angle     :  0.584  10.798  12874  Z= 0.307
  Chirality :  0.039   0.195   1486
  Planarity :  0.004   0.043   1632
  Dihedral  :  5.437  46.508   1336
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 29.60 %
    Favored  : 67.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.24 (0.25), residues: 1170
  helix:  2.09 (0.19), residues: 756
  sheet:  0.33 (0.61), residues: 62
  loop : -2.03 (0.29), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 584 
 TYR   0.012   0.001   TYR B 536 
 PHE   0.011   0.001   PHE A 325 
 TRP   0.043   0.002   TRP A 822 
 HIS   0.003   0.001   HIS B 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 9496)
  covalent geometry    : angle       0.58412 (12874)
  hydrogen bonds       : bond        0.06694 (  613)
  hydrogen bonds       : angle       4.22521 ( 1818)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 94
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  822 TRP cc_start: 0.8921 (p-90) cc_final: 0.8573 (p-90)
REVERT: B  455 ASP cc_start: 0.9242 (m-30) cc_final: 0.8729 (p0)
REVERT: B  562 GLU cc_start: 0.9564 (tp30) cc_final: 0.9139 (mm-30)
REVERT: B  566 ASP cc_start: 0.9696 (t0) cc_final: 0.9495 (t0)
REVERT: B  635 LEU cc_start: 0.9633 (mm) cc_final: 0.9411 (mm)
REVERT: B  739 ARG cc_start: 0.9299 (OUTLIER) cc_final: 0.9076 (ptp-170)
  outliers start: 30
  outliers final: 23
  residues processed: 119
  average time/residue: 0.0672
  time to fit residues: 12.7016
Evaluate side-chains
  112 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 88
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  354 HIS
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain A residue  630 SER
Chi-restraints excluded: chain A residue  654 ILE
Chi-restraints excluded: chain A residue  676 PHE
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  750 LEU
Chi-restraints excluded: chain A residue  754 THR
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  258 SER
Chi-restraints excluded: chain B residue  354 HIS
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  444 THR
Chi-restraints excluded: chain B residue  505 ILE
Chi-restraints excluded: chain B residue  584 ARG
Chi-restraints excluded: chain B residue  614 MET
Chi-restraints excluded: chain B residue  739 ARG
Chi-restraints excluded: chain B residue  742 LEU
Chi-restraints excluded: chain B residue  811 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   chunk 7 optimal weight:    6.9990
   chunk 48 optimal weight:    5.9990
   chunk 50 optimal weight:    5.9990
   chunk 51 optimal weight:    4.9990
   chunk 73 optimal weight:    6.9990
   chunk 22 optimal weight:    4.9990
   chunk 85 optimal weight:    1.9990
   chunk 101 optimal weight:   10.0000
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 783 HIS
B 808 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.075632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.053517 restraints weight = 38920.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.2981 rms_B_bonded: 5.39
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2978
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2978 r_free = 0.2978    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2978 r_free = 0.2978    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2978
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8616
moved from start:          0.3382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   9496  Z= 0.223
  Angle     :  0.628  10.804  12874  Z= 0.336
  Chirality :  0.040   0.216   1486
  Planarity :  0.004   0.046   1632
  Dihedral  :  5.303  42.425   1336
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 27.88 %
    Favored  : 67.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.12 (0.24), residues: 1170
  helix:  1.95 (0.19), residues: 756
  sheet:  0.07 (0.61), residues: 62
  loop : -1.94 (0.30), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 663 
 TYR   0.017   0.002   TYR B 465 
 PHE   0.030   0.002   PHE B 637 
 TRP   0.027   0.002   TRP A 822 
 HIS   0.005   0.001   HIS A 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 ( 9496)
  covalent geometry    : angle       0.62788 (12874)
  hydrogen bonds       : bond        0.07280 (  613)
  hydrogen bonds       : angle       4.46940 ( 1818)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 88
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  355 GLU cc_start: 0.9381 (OUTLIER) cc_final: 0.8979 (tp30)
REVERT: A  822 TRP cc_start: 0.8758 (p-90) cc_final: 0.8440 (p-90)
REVERT: B  455 ASP cc_start: 0.9326 (m-30) cc_final: 0.9014 (p0)
REVERT: B  562 GLU cc_start: 0.9603 (tp30) cc_final: 0.9096 (tm-30)
REVERT: B  635 LEU cc_start: 0.9693 (mm) cc_final: 0.9455 (mm)
REVERT: B  710 MET cc_start: 0.9560 (mmt) cc_final: 0.9265 (mpp)
  outliers start: 48
  outliers final: 32
  residues processed: 125
  average time/residue: 0.0649
  time to fit residues: 12.3508
Evaluate side-chains
  115 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 82
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  354 HIS
Chi-restraints excluded: chain A residue  355 GLU
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  461 GLU
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain A residue  565 PHE
Chi-restraints excluded: chain A residue  630 SER
Chi-restraints excluded: chain A residue  676 PHE
Chi-restraints excluded: chain A residue  686 TYR
Chi-restraints excluded: chain A residue  739 ARG
Chi-restraints excluded: chain A residue  742 LEU
Chi-restraints excluded: chain A residue  750 LEU
Chi-restraints excluded: chain A residue  754 THR
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  258 SER
Chi-restraints excluded: chain B residue  354 HIS
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  422 SER
Chi-restraints excluded: chain B residue  444 THR
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  505 ILE
Chi-restraints excluded: chain B residue  565 PHE
Chi-restraints excluded: chain B residue  584 ARG
Chi-restraints excluded: chain B residue  614 MET
Chi-restraints excluded: chain B residue  739 ARG
Chi-restraints excluded: chain B residue  742 LEU
Chi-restraints excluded: chain B residue  811 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 103 optimal weight:    2.9990
   chunk 46 optimal weight:   10.0000
   chunk 24 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 95 optimal weight:    7.9990
   chunk 15 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 80 optimal weight:    0.9980
   chunk 72 optimal weight:    0.6980
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
B 279 ASN
B 733 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.078053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.055270 restraints weight = 38815.869|
|-----------------------------------------------------------------------------|
r_work (start): 0.3023 rms_B_bonded: 5.56
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3024
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3024
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8577
moved from start:          0.3554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9496  Z= 0.141
  Angle     :  0.583  11.930  12874  Z= 0.299
  Chirality :  0.039   0.219   1486
  Planarity :  0.003   0.044   1632
  Dihedral  :  5.104  43.006   1336
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 29.70 %
    Favored  : 66.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.36 (0.25), residues: 1170
  helix:  2.15 (0.19), residues: 760
  sheet:  0.08 (0.61), residues: 62
  loop : -1.88 (0.30), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 584 
 TYR   0.011   0.001   TYR B 465 
 PHE   0.017   0.001   PHE B 418 
 TRP   0.024   0.002   TRP A 822 
 HIS   0.002   0.001   HIS B 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 9496)
  covalent geometry    : angle       0.58330 (12874)
  hydrogen bonds       : bond        0.06454 (  613)
  hydrogen bonds       : angle       4.13660 ( 1818)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 90
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  822 TRP cc_start: 0.8770 (p-90) cc_final: 0.8341 (p-90)
REVERT: B  455 ASP cc_start: 0.9266 (m-30) cc_final: 0.8951 (p0)
REVERT: B  562 GLU cc_start: 0.9582 (tp30) cc_final: 0.9133 (mm-30)
REVERT: B  635 LEU cc_start: 0.9674 (mm) cc_final: 0.9411 (mm)
REVERT: B  710 MET cc_start: 0.9569 (mmt) cc_final: 0.9279 (mpp)
  outliers start: 37
  outliers final: 26
  residues processed: 121
  average time/residue: 0.0668
  time to fit residues: 12.7021
Evaluate side-chains
  114 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 88
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain A residue  354 HIS
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  444 THR
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain A residue  565 PHE
Chi-restraints excluded: chain A residue  630 SER
Chi-restraints excluded: chain A residue  652 GLN
Chi-restraints excluded: chain A residue  654 ILE
Chi-restraints excluded: chain A residue  676 PHE
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  739 ARG
Chi-restraints excluded: chain A residue  742 LEU
Chi-restraints excluded: chain A residue  750 LEU
Chi-restraints excluded: chain A residue  754 THR
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  258 SER
Chi-restraints excluded: chain B residue  354 HIS
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  422 SER
Chi-restraints excluded: chain B residue  531 VAL
Chi-restraints excluded: chain B residue  565 PHE
Chi-restraints excluded: chain B residue  614 MET
Chi-restraints excluded: chain B residue  742 LEU
Chi-restraints excluded: chain B residue  811 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 38 optimal weight:   10.0000
   chunk 102 optimal weight:   10.0000
   chunk 23 optimal weight:    5.9990
   chunk 34 optimal weight:    9.9990
   chunk 43 optimal weight:    7.9990
   chunk 35 optimal weight:    5.9990
   chunk 69 optimal weight:    0.9990
   chunk 115 optimal weight:    0.0010
   chunk 91 optimal weight:    0.7980
   overall best weight:    1.3390

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.077616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.055181 restraints weight = 37925.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.3070 rms_B_bonded: 5.17
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3071
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3071 r_free = 0.3071    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3071 r_free = 0.3071    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.3071
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8569
moved from start:          0.3701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9496  Z= 0.135
  Angle     :  0.594  15.055  12874  Z= 0.300
  Chirality :  0.039   0.232   1486
  Planarity :  0.003   0.043   1632
  Dihedral  :  4.898  41.832   1334
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 31.01 %
    Favored  : 65.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.40 (0.25), residues: 1170
  helix:  2.19 (0.19), residues: 760
  sheet:  0.03 (0.61), residues: 62
  loop : -1.90 (0.30), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 634 
 TYR   0.011   0.001   TYR B 465 
 PHE   0.014   0.001   PHE B 418 
 TRP   0.022   0.002   TRP A 822 
 HIS   0.002   0.001   HIS B 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 9496)
  covalent geometry    : angle       0.59391 (12874)
  hydrogen bonds       : bond        0.06146 (  613)
  hydrogen bonds       : angle       4.05258 ( 1818)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 88
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  822 TRP cc_start: 0.8788 (p-90) cc_final: 0.8346 (p-90)
REVERT: B  455 ASP cc_start: 0.9177 (m-30) cc_final: 0.8839 (p0)
REVERT: B  562 GLU cc_start: 0.9550 (tp30) cc_final: 0.9089 (tm-30)
REVERT: B  635 LEU cc_start: 0.9701 (mm) cc_final: 0.9405 (mm)
REVERT: B  710 MET cc_start: 0.9555 (mmt) cc_final: 0.9276 (mpp)
  outliers start: 30
  outliers final: 24
  residues processed: 116
  average time/residue: 0.0698
  time to fit residues: 13.0651
Evaluate side-chains
  104 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 80
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain A residue  354 HIS
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain A residue  652 GLN
Chi-restraints excluded: chain A residue  654 ILE
Chi-restraints excluded: chain A residue  676 PHE
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  739 ARG
Chi-restraints excluded: chain A residue  742 LEU
Chi-restraints excluded: chain A residue  750 LEU
Chi-restraints excluded: chain A residue  754 THR
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  258 SER
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  354 HIS
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  422 SER
Chi-restraints excluded: chain B residue  531 VAL
Chi-restraints excluded: chain B residue  565 PHE
Chi-restraints excluded: chain B residue  614 MET
Chi-restraints excluded: chain B residue  742 LEU
Chi-restraints excluded: chain B residue  811 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 37 optimal weight:   10.0000
   chunk 50 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 103 optimal weight:    5.9990
   chunk 47 optimal weight:    8.9990
   chunk 56 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 54 optimal weight:    5.9990
   chunk 67 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 68 optimal weight:    0.8980
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.079497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.058216 restraints weight = 36266.311|
|-----------------------------------------------------------------------------|
r_work (start): 0.3077 rms_B_bonded: 5.10
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.3838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9496  Z= 0.153
  Angle     :  0.606  13.621  12874  Z= 0.308
  Chirality :  0.040   0.237   1486
  Planarity :  0.003   0.041   1632
  Dihedral  :  4.786  40.449   1334
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 31.01 %
    Favored  : 65.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.40 (0.25), residues: 1170
  helix:  2.18 (0.19), residues: 760
  sheet: -0.06 (0.60), residues: 62
  loop : -1.84 (0.30), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 452 
 TYR   0.013   0.001   TYR B 465 
 PHE   0.014   0.001   PHE A 325 
 TRP   0.021   0.001   TRP A 822 
 HIS   0.003   0.001   HIS B 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 9496)
  covalent geometry    : angle       0.60637 (12874)
  hydrogen bonds       : bond        0.06180 (  613)
  hydrogen bonds       : angle       4.10393 ( 1818)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 82
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 GLN cc_start: 0.9545 (OUTLIER) cc_final: 0.8958 (pp30)
REVERT: A  442 MET cc_start: 0.9297 (tmm) cc_final: 0.9020 (tmm)
REVERT: A  650 ASP cc_start: 0.9016 (OUTLIER) cc_final: 0.8698 (m-30)
REVERT: A  822 TRP cc_start: 0.8755 (p-90) cc_final: 0.8367 (p-90)
REVERT: B  562 GLU cc_start: 0.9518 (tp30) cc_final: 0.9067 (tm-30)
REVERT: B  635 LEU cc_start: 0.9701 (mm) cc_final: 0.9435 (mm)
REVERT: B  710 MET cc_start: 0.9538 (mmt) cc_final: 0.9319 (mpp)
  outliers start: 30
  outliers final: 26
  residues processed: 111
  average time/residue: 0.0717
  time to fit residues: 12.5899
Evaluate side-chains
  108 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 80
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain A residue  338 GLN
Chi-restraints excluded: chain A residue  354 HIS
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain A residue  565 PHE
Chi-restraints excluded: chain A residue  650 ASP
Chi-restraints excluded: chain A residue  652 GLN
Chi-restraints excluded: chain A residue  654 ILE
Chi-restraints excluded: chain A residue  676 PHE
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  739 ARG
Chi-restraints excluded: chain A residue  742 LEU
Chi-restraints excluded: chain A residue  750 LEU
Chi-restraints excluded: chain A residue  754 THR
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  258 SER
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  354 HIS
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  422 SER
Chi-restraints excluded: chain B residue  531 VAL
Chi-restraints excluded: chain B residue  565 PHE
Chi-restraints excluded: chain B residue  614 MET
Chi-restraints excluded: chain B residue  742 LEU
Chi-restraints excluded: chain B residue  811 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 109 optimal weight:   20.0000
   chunk 28 optimal weight:    0.7980
   chunk 61 optimal weight:    6.9990
   chunk 52 optimal weight:    5.9990
   chunk 4 optimal weight:    0.7980
   chunk 111 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   chunk 102 optimal weight:   10.0000
   chunk 56 optimal weight:    0.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.079100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.056636 restraints weight = 37704.832|
|-----------------------------------------------------------------------------|
r_work (start): 0.3103 rms_B_bonded: 5.34
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
moved from start:          0.4028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9496  Z= 0.127
  Angle     :  0.611  13.697  12874  Z= 0.302
  Chirality :  0.040   0.249   1486
  Planarity :  0.003   0.042   1632
  Dihedral  :  4.762  39.439   1334
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 31.72 %
    Favored  : 65.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.50 (0.25), residues: 1170
  helix:  2.26 (0.19), residues: 758
  sheet: -0.03 (0.59), residues: 62
  loop : -1.79 (0.30), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 634 
 TYR   0.009   0.001   TYR B 465 
 PHE   0.014   0.001   PHE B 418 
 TRP   0.024   0.002   TRP A 822 
 HIS   0.002   0.001   HIS A 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 9496)
  covalent geometry    : angle       0.61138 (12874)
  hydrogen bonds       : bond        0.05622 (  613)
  hydrogen bonds       : angle       3.95968 ( 1818)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 87
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 GLN cc_start: 0.9538 (OUTLIER) cc_final: 0.8941 (pp30)
REVERT: A  442 MET cc_start: 0.9281 (tmm) cc_final: 0.9028 (tmm)
REVERT: A  822 TRP cc_start: 0.8853 (p-90) cc_final: 0.8459 (p-90)
REVERT: B  338 GLN cc_start: 0.9539 (OUTLIER) cc_final: 0.8950 (pp30)
REVERT: B  455 ASP cc_start: 0.8512 (p0) cc_final: 0.8290 (p0)
REVERT: B  562 GLU cc_start: 0.9581 (tp30) cc_final: 0.9101 (tm-30)
REVERT: B  635 LEU cc_start: 0.9659 (mm) cc_final: 0.9386 (mm)
REVERT: B  710 MET cc_start: 0.9583 (mmt) cc_final: 0.9348 (mpp)
  outliers start: 27
  outliers final: 16
  residues processed: 112
  average time/residue: 0.0612
  time to fit residues: 11.1431
Evaluate side-chains
  101 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 83
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  338 GLN
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain A residue  652 GLN
Chi-restraints excluded: chain A residue  654 ILE
Chi-restraints excluded: chain A residue  742 LEU
Chi-restraints excluded: chain A residue  754 THR
Chi-restraints excluded: chain B residue  258 SER
Chi-restraints excluded: chain B residue  289 ILE
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  338 GLN
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  422 SER
Chi-restraints excluded: chain B residue  531 VAL
Chi-restraints excluded: chain B residue  614 MET
Chi-restraints excluded: chain B residue  742 LEU
Chi-restraints excluded: chain B residue  811 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 56 optimal weight:    4.9990
   chunk 78 optimal weight:    5.9990
   chunk 94 optimal weight:    0.9990
   chunk 29 optimal weight:    4.9990
   chunk 12 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9980
   chunk 112 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   chunk 77 optimal weight:    7.9990
   chunk 115 optimal weight:    0.0020
   chunk 7 optimal weight:    7.9990
   overall best weight:    0.6790

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

Flipped N/Q/H residues before XYZ refinement:
** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.079416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.057199 restraints weight = 37019.047|
|-----------------------------------------------------------------------------|
r_work (start): 0.3132 rms_B_bonded: 5.09
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8509
moved from start:          0.4148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9496  Z= 0.128
  Angle     :  0.630  12.926  12874  Z= 0.309
  Chirality :  0.040   0.251   1486
  Planarity :  0.003   0.043   1632
  Dihedral  :  4.700  38.875   1334
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 33.13 %
    Favored  : 65.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.57 (0.25), residues: 1170
  helix:  2.32 (0.19), residues: 752
  sheet:  0.07 (0.59), residues: 62
  loop : -1.73 (0.30), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 634 
 TYR   0.010   0.001   TYR B 465 
 PHE   0.015   0.001   PHE A 325 
 TRP   0.023   0.001   TRP A 822 
 HIS   0.002   0.001   HIS A 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 9496)
  covalent geometry    : angle       0.62994 (12874)
  hydrogen bonds       : bond        0.05434 (  613)
  hydrogen bonds       : angle       3.94694 ( 1818)

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

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

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2340 Ramachandran restraints generated.
    1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 GLN cc_start: 0.9538 (OUTLIER) cc_final: 0.8935 (pp30)
REVERT: A  442 MET cc_start: 0.9284 (tmm) cc_final: 0.9044 (tmm)
REVERT: A  652 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8531 (mp10)
REVERT: A  822 TRP cc_start: 0.8836 (p-90) cc_final: 0.8459 (p-90)
REVERT: B  455 ASP cc_start: 0.8530 (p0) cc_final: 0.8297 (p0)
REVERT: B  562 GLU cc_start: 0.9549 (tp30) cc_final: 0.9103 (tm-30)
REVERT: B  635 LEU cc_start: 0.9635 (mm) cc_final: 0.9339 (mm)
REVERT: B  710 MET cc_start: 0.9564 (mmt) cc_final: 0.9333 (mpp)
  outliers start: 14
  outliers final: 9
  residues processed: 98
  average time/residue: 0.0637
  time to fit residues: 10.3553
Evaluate side-chains
  93 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  338 GLN
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  652 GLN
Chi-restraints excluded: chain A residue  654 ILE
Chi-restraints excluded: chain A residue  742 LEU
Chi-restraints excluded: chain A residue  754 THR
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  742 LEU
Chi-restraints excluded: chain B residue  811 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 35 optimal weight:    9.9990
   chunk 115 optimal weight:    0.7980
   chunk 94 optimal weight:   20.0000
   chunk 44 optimal weight:    9.9990
   chunk 73 optimal weight:    7.9990
   chunk 57 optimal weight:    7.9990
   chunk 95 optimal weight:    9.9990
   chunk 4 optimal weight:    1.9990
   chunk 104 optimal weight:    7.9990
   chunk 21 optimal weight:    0.7980
   chunk 55 optimal weight:    5.9990
   overall best weight:    3.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 459 ASN
** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.075717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.054179 restraints weight = 37081.839|
|-----------------------------------------------------------------------------|
r_work (start): 0.3029 rms_B_bonded: 4.81
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8609
moved from start:          0.4189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   9496  Z= 0.213
  Angle     :  0.685  16.111  12874  Z= 0.345
  Chirality :  0.042   0.229   1486
  Planarity :  0.004   0.063   1632
  Dihedral  :  4.759  39.679   1334
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 33.13 %
    Favored  : 64.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.37 (0.25), residues: 1170
  helix:  2.13 (0.19), residues: 756
  sheet: -0.14 (0.59), residues: 62
  loop : -1.72 (0.30), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 634 
 TYR   0.014   0.001   TYR B 465 
 PHE   0.020   0.001   PHE A 418 
 TRP   0.020   0.002   TRP A 546 
 HIS   0.004   0.001   HIS A 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 ( 9496)
  covalent geometry    : angle       0.68451 (12874)
  hydrogen bonds       : bond        0.06501 (  613)
  hydrogen bonds       : angle       4.26332 ( 1818)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1661.55 seconds
wall clock time: 29 minutes 17.92 seconds (1757.92 seconds total)