Starting phenix.real_space_refine
on Wed Mar  4 00:06:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7dny_30790/03_2026/7dny_30790.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7dny_30790/03_2026/7dny_30790.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7dny_30790/03_2026/7dny_30790.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7dny_30790/03_2026/7dny_30790.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7dny_30790/03_2026/7dny_30790.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7dny_30790/03_2026/7dny_30790.map"
  }
  resolution = 3.4
  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=   0.000 sd=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      34      5.16       5
     C    5968      2.51       5
     N    1557      2.21       5
     O    1662      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9221
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4482
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 571, 4482
          Classifications: {'peptide': 571}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 12, 'TRANS': 558}
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'GLU:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 22
    Chain: "B"
      Number of atoms: 4516
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 575, 4516
          Classifications: {'peptide': 575}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 13, 'TRANS': 561}
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "A"
      Number of atoms: 153
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 153
          Unusual residues: {'HT9': 1, 'Y01': 3}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "B"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 70
          Unusual residues: {'Y01': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.20, per 1000 atoms: 0.24
  Number of scatterers: 9221
  At special positions: 0
  Unit cell: (68.88, 101.68, 137.104, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      34     16.00
     O    1662      8.00
     N    1557      7.00
     C    5968      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: 0.67
  Conformation dependent library (CDL) restraints added in 364.1 milliseconds
  

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2110

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 8 sheets defined
      72.2% alpha, 4.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 258 through 295
      removed outlier: 3.717A  pdb=" N   GLN A 262 " --> pdb=" O   SER A 258 " (cutoff:3.500A)
      Proline residue:  A 283  - end of helix
      removed outlier: 3.600A  pdb=" N   GLU A 295 " --> pdb=" O   ASN A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 317
      removed outlier: 4.463A  pdb=" N   TRP A 304 " --> pdb=" O   ASN A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 334
    Processing helix  chain 'A' and resid 334 through 355
      removed outlier: 3.913A  pdb=" N   PHE A 340 " --> pdb=" O   ARG A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 363
      removed outlier: 3.605A  pdb=" N   GLY A 363 " --> pdb=" O   ARG A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 390
      removed outlier: 3.515A  pdb=" N   VAL A 369 " --> pdb=" O   ARG A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 408
    Processing helix  chain 'A' and resid 410 through 459
      removed outlier: 4.099A  pdb=" N   GLY A 414 " --> pdb=" O   ASN A 410 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   ALA A 453 " --> pdb=" O   THR A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 467
    Processing helix  chain 'A' and resid 468 through 522
    Processing helix  chain 'A' and resid 526 through 570
      removed outlier: 4.155A  pdb=" N   TYR A 530 " --> pdb=" O   GLN A 526 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   VAL A 531 " --> pdb=" O   VAL A 527 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   ILE A 538 " --> pdb=" O   GLY A 534 " (cutoff:3.500A)
      Proline residue:  A 543  - end of helix
      removed outlier: 4.064A  pdb=" N   TRP A 546 " --> pdb=" O   MET A 542 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   GLY A 548 " --> pdb=" O   LEU A 544 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   THR A 549 " --> pdb=" O   ASN A 545 " (cutoff:3.500A)
      removed outlier: 4.897A  pdb=" N   GLN A 555 " --> pdb=" O   TYR A 551 " (cutoff:3.500A)
      removed outlier: 4.455A  pdb=" N   THR A 556 " --> pdb=" O   ARG A 552 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   GLU A 570 " --> pdb=" O   ASP A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 629 through 637
      removed outlier: 4.062A  pdb=" N   LEU A 633 " --> pdb=" O   LYS A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 658 through 664
      removed outlier: 3.844A  pdb=" N   LEU A 662 " --> pdb=" O   THR A 658 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   SER A 664 " --> pdb=" O   ALA A 660 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 688
      removed outlier: 3.720A  pdb=" N   GLY A 687 " --> pdb=" O   ASN A 683 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   ARG A 688 " --> pdb=" O   ILE A 684 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 692 through 703
    Processing helix  chain 'A' and resid 705 through 712
    Processing helix  chain 'A' and resid 714 through 718
      removed outlier: 3.590A  pdb=" N   ARG A 717 " --> pdb=" O   GLU A 714 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   THR A 718 " --> pdb=" O   GLY A 715 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 714 through 718'
    Processing helix  chain 'A' and resid 728 through 744
    Processing helix  chain 'A' and resid 758 through 773
    Processing helix  chain 'A' and resid 785 through 790
    Processing helix  chain 'A' and resid 807 through 815
    Processing helix  chain 'A' and resid 816 through 827
    Processing helix  chain 'B' and resid 258 through 295
      removed outlier: 4.546A  pdb=" N   VAL B 280 " --> pdb=" O   ARG B 276 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LEU B 281 " --> pdb=" O   ALA B 277 " (cutoff:3.500A)
      Proline residue:  B 283  - end of helix
    Processing helix  chain 'B' and resid 298 through 316
      removed outlier: 3.969A  pdb=" N   TRP B 304 " --> pdb=" O   ASN B 300 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 324 through 356
      removed outlier: 4.515A  pdb=" N   ARG B 336 " --> pdb=" O   PHE B 332 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   VAL B 337 " --> pdb=" O   LEU B 333 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   PHE B 340 " --> pdb=" O   ARG B 336 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 357 through 362
      removed outlier: 3.620A  pdb=" N   HIS B 361 " --> pdb=" O   SER B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 408
      removed outlier: 4.487A  pdb=" N   ILE B 372 " --> pdb=" O   GLU B 368 " (cutoff:3.500A)
      removed outlier: 4.871A  pdb=" N   ILE B 392 " --> pdb=" O   VAL B 388 " (cutoff:3.500A)
      Proline residue:  B 393  - end of helix
    Processing helix  chain 'B' and resid 410 through 459
      removed outlier: 3.545A  pdb=" N   GLY B 414 " --> pdb=" O   ASN B 410 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 459 through 466
    Processing helix  chain 'B' and resid 468 through 522
      removed outlier: 4.196A  pdb=" N   LYS B 489 " --> pdb=" O   GLY B 485 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 526 through 542
      removed outlier: 3.669A  pdb=" N   TYR B 530 " --> pdb=" O   GLN B 526 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ILE B 538 " --> pdb=" O   GLY B 534 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 543 through 553
    Processing helix  chain 'B' and resid 553 through 570
      removed outlier: 4.207A  pdb=" N   ASN B 557 " --> pdb=" O   MET B 553 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLU B 562 " --> pdb=" O   PHE B 558 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 627 through 637
    Processing helix  chain 'B' and resid 658 through 666
    Processing helix  chain 'B' and resid 680 through 685
    Processing helix  chain 'B' and resid 686 through 688
      No H-bonds generated for 'chain 'B' and resid 686 through 688'
    Processing helix  chain 'B' and resid 692 through 704
    Processing helix  chain 'B' and resid 705 through 712
    Processing helix  chain 'B' and resid 714 through 718
      removed outlier: 3.730A  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
      removed outlier: 3.759A  pdb=" N   ALA B 764 " --> pdb=" O   SER B 760 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 784 through 790
      removed outlier: 3.553A  pdb=" N   ASN B 790 " --> pdb=" O   SER B 786 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 807 through 815
    Processing helix  chain 'B' and resid 816 through 827
    Processing sheet with id=AA1, first strand: chain 'A' and resid 606 through 607
      removed outlier: 3.515A  pdb=" N   PHE A 597 " --> pdb=" O   LEU A 606 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   PHE A 611 " --> pdb=" O   PHE A 592 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 606 through 607
      removed outlier: 3.515A  pdb=" N   PHE A 597 " --> pdb=" O   LEU A 606 " (cutoff:3.500A)
      removed outlier: 5.013A  pdb=" N   PHE A 592 " --> pdb=" O   ARG A 648 " (cutoff:3.500A)
      removed outlier: 7.237A  pdb=" N   ARG A 648 " --> pdb=" O   PHE A 592 " (cutoff:3.500A)
      removed outlier: 5.234A  pdb=" N   ASN A 594 " --> pdb=" O   CYS A 646 " (cutoff:3.500A)
      removed outlier: 4.701A  pdb=" N   CYS A 646 " --> pdb=" O   ASN A 594 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 619 through 621
      removed outlier: 6.900A  pdb=" N   LEU A 619 " --> pdb=" O   VAL A 780 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   VAL A 781 " --> pdb=" O   LEU A 750 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 666 through 667
    Processing sheet with id=AA5, first strand: chain 'A' and resid 795 through 798
      removed outlier: 6.958A  pdb=" N   VAL A 796 " --> pdb=" O   VAL A 803 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 595 through 597
      removed outlier: 3.672A  pdb=" N   VAL B 595 " --> pdb=" O   VAL B 609 " (cutoff:3.500A)
      removed outlier: 7.580A  pdb=" N   PHE B 597 " --> pdb=" O   GLN B 607 " (cutoff:3.500A)
      removed outlier: 5.203A  pdb=" N   GLN B 607 " --> pdb=" O   PHE B 597 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 619 through 620
    Processing sheet with id=AA8, first strand: chain 'B' and resid 796 through 798
      removed outlier: 7.321A  pdb=" N   VAL B 796 " --> pdb=" O   VAL B 803 " (cutoff:3.500A)

    615 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: 1.48

  Time building geometry restraints manager: 0.88 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1549
        1.32 -     1.45: 2494
        1.45 -     1.57: 5313
        1.57 -     1.70: 1
        1.70 -     1.82: 56
  Bond restraints: 9413
  Sorted by residual:
  bond pdb=" N   ILE A 747 "
       pdb=" CA  ILE A 747 "
    ideal  model  delta    sigma   weight residual
    1.456  1.496 -0.039 1.14e-02 7.69e+03 1.19e+01
  bond pdb=" N   THR B 320 "
       pdb=" CA  THR B 320 "
    ideal  model  delta    sigma   weight residual
    1.456  1.496 -0.039 1.23e-02 6.61e+03 1.03e+01
  bond pdb=" N   VAL B 527 "
       pdb=" CA  VAL B 527 "
    ideal  model  delta    sigma   weight residual
    1.459  1.499 -0.040 1.25e-02 6.40e+03 1.00e+01
  bond pdb=" N   ILE B 705 "
       pdb=" CA  ILE B 705 "
    ideal  model  delta    sigma   weight residual
    1.459  1.498 -0.040 1.25e-02 6.40e+03 1.00e+01
  bond pdb=" N   ALA A 744 "
       pdb=" CA  ALA A 744 "
    ideal  model  delta    sigma   weight residual
    1.457  1.485 -0.029 9.10e-03 1.21e+04 9.84e+00
  ... (remaining 9408 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.98: 12358
        2.98 -     5.96: 385
        5.96 -     8.94: 54
        8.94 -    11.92: 8
       11.92 -    14.89: 2
  Bond angle restraints: 12807
  Sorted by residual:
  angle pdb=" CA  GLY B 324 "
        pdb=" C   GLY B 324 "
        pdb=" O   GLY B 324 "
      ideal   model   delta    sigma   weight residual
     122.37  118.09    4.28 7.30e-01 1.88e+00 3.43e+01
  angle pdb=" C   THR B 320 "
        pdb=" CA  THR B 320 "
        pdb=" CB  THR B 320 "
      ideal   model   delta    sigma   weight residual
     110.06  117.37   -7.31 1.44e+00 4.82e-01 2.58e+01
  angle pdb=" CB  ARG A 452 "
        pdb=" CG  ARG A 452 "
        pdb=" CD  ARG A 452 "
      ideal   model   delta    sigma   weight residual
     111.30  122.91  -11.61 2.30e+00 1.89e-01 2.55e+01
  angle pdb=" N   PHE B 409 "
        pdb=" CA  PHE B 409 "
        pdb=" C   PHE B 409 "
      ideal   model   delta    sigma   weight residual
     109.18  102.13    7.05 1.42e+00 4.96e-01 2.47e+01
  angle pdb=" CB  MET A 442 "
        pdb=" CG  MET A 442 "
        pdb=" SD  MET A 442 "
      ideal   model   delta    sigma   weight residual
     112.70   97.81   14.89 3.00e+00 1.11e-01 2.46e+01
  ... (remaining 12802 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.66: 5107
       17.66 -    35.32: 542
       35.32 -    52.98: 97
       52.98 -    70.63: 23
       70.63 -    88.29: 12
  Dihedral angle restraints: 5781
    sinusoidal: 2487
      harmonic: 3294
  Sorted by residual:
  dihedral pdb=" CA  ARG A 814 "
           pdb=" C   ARG A 814 "
           pdb=" N   GLY A 815 "
           pdb=" CA  GLY A 815 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.69   26.31     0      5.00e+00 4.00e-02 2.77e+01
  dihedral pdb=" CA  GLU A 591 "
           pdb=" C   GLU A 591 "
           pdb=" N   PHE A 592 "
           pdb=" CA  PHE A 592 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.23   25.77     0      5.00e+00 4.00e-02 2.66e+01
  dihedral pdb=" CA  LEU A 353 "
           pdb=" C   LEU A 353 "
           pdb=" N   HIS A 354 "
           pdb=" CA  HIS A 354 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.07   24.93     0      5.00e+00 4.00e-02 2.49e+01
  ... (remaining 5778 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.083: 1188
       0.083 -    0.166: 254
       0.166 -    0.249: 37
       0.249 -    0.332: 7
       0.332 -    0.416: 2
  Chirality restraints: 1488
  Sorted by residual:
  chirality pdb=" CB  VAL B 696 "
            pdb=" CA  VAL B 696 "
            pdb=" CG1 VAL B 696 "
            pdb=" CG2 VAL B 696 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.21   -0.42 2.00e-01 2.50e+01 4.32e+00
  chirality pdb=" CG  LEU B 769 "
            pdb=" CB  LEU B 769 "
            pdb=" CD1 LEU B 769 "
            pdb=" CD2 LEU B 769 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.24   -0.35 2.00e-01 2.50e+01 3.11e+00
  chirality pdb=" CB  VAL A 388 "
            pdb=" CA  VAL A 388 "
            pdb=" CG1 VAL A 388 "
            pdb=" CG2 VAL A 388 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.30   -0.33 2.00e-01 2.50e+01 2.66e+00
  ... (remaining 1485 not shown)

  Planarity restraints: 1592
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 HT9 A 904 "   -0.065 2.00e-02 2.50e+03   1.85e-01 7.71e+02
        pdb=" C11 HT9 A 904 "    0.080 2.00e-02 2.50e+03
        pdb=" C12 HT9 A 904 "   -0.045 2.00e-02 2.50e+03
        pdb=" C13 HT9 A 904 "    0.062 2.00e-02 2.50e+03
        pdb=" C14 HT9 A 904 "   -0.262 2.00e-02 2.50e+03
        pdb=" C20 HT9 A 904 "    0.144 2.00e-02 2.50e+03
        pdb=" C21 HT9 A 904 "    0.313 2.00e-02 2.50e+03
        pdb=" C35 HT9 A 904 "   -0.312 2.00e-02 2.50e+03
        pdb=" N3  HT9 A 904 "    0.084 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 299 "   -0.037 2.00e-02 2.50e+03   3.06e-02 2.34e+01
        pdb=" CG  TRP A 299 "    0.078 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 299 "   -0.039 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 299 "    0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 299 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 299 "    0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 299 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 299 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 299 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 299 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B 542 "    0.060 5.00e-02 4.00e+02   9.03e-02 1.31e+01
        pdb=" N   PRO B 543 "   -0.156 5.00e-02 4.00e+02
        pdb=" CA  PRO B 543 "    0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO B 543 "    0.050 5.00e-02 4.00e+02
  ... (remaining 1589 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 963
        2.74 -     3.28: 9759
        3.28 -     3.82: 16047
        3.82 -     4.36: 18156
        4.36 -     4.90: 29758
  Nonbonded interactions: 74683
  Sorted by model distance:
  nonbonded pdb=" O   THR B 428 "
            pdb=" OG1 THR B 432 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" O   ILE A 402 "
            pdb=" OG  SER A 406 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" OG1 THR A 449 "
            pdb=" NH2 ARG A 452 "
     model   vdw
     2.303 3.120
  nonbonded pdb=" OD1 ASN A 459 "
            pdb=" OG1 THR A 462 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" OE1 GLN B 701 "
            pdb=" OH  TYR B 716 "
     model   vdw
     2.308 3.040
  ... (remaining 74678 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 258 through 357 or (resid 358 through 359 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 360 through 463 or (resid 464  \ 
through 468 and (name N or name CA or name C or name O or name CB )) or resid 46 \ 
9 through 902))
  selection = (chain 'B' and (resid 258 through 465 or (resid 466 through 468 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 469 through 523 or (resid 524  \ 
and (name N or name CA or name C or name O or name CB )) or resid 525 or (resid  \ 
526 and (name N or name CA or name C or name O or name CB )) or resid 527 throug \ 
h 902))
}

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=0.50 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:             3.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.460
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7341
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      :  0.009   0.104   9413  Z= 0.474
  Angle     :  1.248  14.894  12807  Z= 0.742
  Chirality :  0.071   0.416   1488
  Planarity :  0.008   0.185   1592
  Dihedral  : 15.292  88.293   3671
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  1.46 %
    Favored  : 97.49 %
  Cbeta Deviations :  0.09 %
  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: -1.83 (0.22), residues: 1142
  helix: -0.53 (0.17), residues: 769
  sheet: -2.07 (0.64), residues: 53
  loop : -2.49 (0.28), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.023   0.001   ARG A 452 
 TYR   0.042   0.004   TYR A 465 
 PHE   0.051   0.004   PHE A 405 
 TRP   0.078   0.005   TRP A 299 
 HIS   0.007   0.001   HIS B 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00893 ( 9413)
  covalent geometry    : angle       1.24809 (12807)
  hydrogen bonds       : bond        0.13638 (  614)
  hydrogen bonds       : angle       6.36132 ( 1818)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 153
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  478 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8188 (tm-30)
REVERT: A  758 ASP cc_start: 0.8140 (m-30) cc_final: 0.7680 (t0)
REVERT: B  309 TYR cc_start: 0.7549 (t80) cc_final: 0.7217 (t80)
REVERT: B  370 LEU cc_start: 0.9107 (tp) cc_final: 0.8906 (tp)
REVERT: B  422 SER cc_start: 0.7976 (m) cc_final: 0.7592 (p)
REVERT: B  466 TYR cc_start: 0.7597 (m-80) cc_final: 0.7279 (m-80)
REVERT: B  646 CYS cc_start: 0.8053 (m) cc_final: 0.7827 (m)
REVERT: B  822 TRP cc_start: 0.8610 (t-100) cc_final: 0.8290 (t-100)
  outliers start: 10
  outliers final: 2
  residues processed: 161
  average time/residue: 0.1057
  time to fit residues: 23.0902
Evaluate side-chains
  113 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 111
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  748 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    8.9990
   chunk 49 optimal weight:   10.0000
   chunk 97 optimal weight:    9.9990
   chunk 113 optimal weight:   10.0000
   chunk 53 optimal weight:    0.0970
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:   20.0000
   chunk 100 optimal weight:    9.9990
   overall best weight:    2.1582

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

Flipped N/Q/H residues before XYZ refinement:
** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5168 r_free = 0.5168 target = 0.212189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4661 r_free = 0.4661 target = 0.158510 restraints weight = 17423.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.4492 rms_B_bonded: 3.12
r_work: 0.4355 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.4355
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4271
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4271 r_free = 0.4271    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4268 r_free = 0.4268    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.4268
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.1475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9413  Z= 0.193
  Angle     :  0.700   8.168  12807  Z= 0.370
  Chirality :  0.043   0.144   1488
  Planarity :  0.005   0.072   1592
  Dihedral  :  8.433  59.730   1641
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 11.49 %
    Favored  : 87.46 %
  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: -0.75 (0.24), residues: 1142
  helix:  0.37 (0.18), residues: 776
  sheet: -2.07 (0.66), residues: 53
  loop : -2.30 (0.30), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 452 
 TYR   0.021   0.002   TYR A 483 
 PHE   0.030   0.002   PHE A 418 
 TRP   0.035   0.002   TRP B 434 
 HIS   0.009   0.001   HIS A 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 9413)
  covalent geometry    : angle       0.69996 (12807)
  hydrogen bonds       : bond        0.05899 (  614)
  hydrogen bonds       : angle       4.88366 ( 1818)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 137
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  286 TYR cc_start: 0.7970 (t80) cc_final: 0.7496 (t80)
REVERT: A  386 TYR cc_start: 0.8512 (t80) cc_final: 0.8122 (t80)
REVERT: A  388 VAL cc_start: 0.8511 (p) cc_final: 0.8259 (p)
REVERT: A  478 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8288 (tm-30)
REVERT: A  561 MET cc_start: 0.7145 (tmm) cc_final: 0.6855 (tmm)
REVERT: A  758 ASP cc_start: 0.8069 (m-30) cc_final: 0.7639 (t0)
REVERT: B  272 MET cc_start: 0.8400 (tmm) cc_final: 0.8149 (tmm)
REVERT: B  309 TYR cc_start: 0.7673 (t80) cc_final: 0.7272 (t80)
REVERT: B  370 LEU cc_start: 0.9166 (tp) cc_final: 0.8957 (tp)
REVERT: B  466 TYR cc_start: 0.7731 (m-80) cc_final: 0.7432 (m-80)
REVERT: B  503 LEU cc_start: 0.8738 (tp) cc_final: 0.8457 (tp)
REVERT: B  646 CYS cc_start: 0.8046 (m) cc_final: 0.7823 (m)
REVERT: B  656 GLN cc_start: 0.8134 (mm110) cc_final: 0.7818 (mp10)
REVERT: B  822 TRP cc_start: 0.8656 (t-100) cc_final: 0.8332 (t-100)
  outliers start: 10
  outliers final: 6
  residues processed: 145
  average time/residue: 0.0879
  time to fit residues: 18.1054
Evaluate side-chains
  124 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 118
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  551 TYR
Chi-restraints excluded: chain A residue  566 ASP
Chi-restraints excluded: chain A residue  748 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 84 optimal weight:    0.7980
   chunk 53 optimal weight:    3.9990
   chunk 37 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 52 optimal weight:    7.9990
   chunk 74 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 90 optimal weight:    7.9990
   chunk 28 optimal weight:    6.9990
   chunk 92 optimal weight:   30.0000
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 445 GLN
A 586 GLN
** B 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5131 r_free = 0.5131 target = 0.208453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4600 r_free = 0.4600 target = 0.154079 restraints weight = 17366.844|
|-----------------------------------------------------------------------------|
r_work (start): 0.4511 rms_B_bonded: 3.06
r_work: 0.4355 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.4355
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4178
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4178 r_free = 0.4178    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4177 r_free = 0.4177    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.4177
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.1865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   9413  Z= 0.229
  Angle     :  0.692   7.347  12807  Z= 0.362
  Chirality :  0.044   0.166   1488
  Planarity :  0.004   0.054   1592
  Dihedral  :  7.974  58.055   1641
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 12.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 15.46 %
    Favored  : 82.03 %
  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: -0.42 (0.24), residues: 1142
  helix:  0.63 (0.18), residues: 769
  sheet: -2.09 (0.65), residues: 53
  loop : -2.10 (0.31), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 723 
 TYR   0.033   0.003   TYR A 465 
 PHE   0.037   0.002   PHE A 418 
 TRP   0.019   0.002   TRP B 434 
 HIS   0.008   0.001   HIS A 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00507 ( 9413)
  covalent geometry    : angle       0.69238 (12807)
  hydrogen bonds       : bond        0.05672 (  614)
  hydrogen bonds       : angle       4.79091 ( 1818)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 123
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  286 TYR cc_start: 0.7984 (t80) cc_final: 0.6894 (t80)
REVERT: A  386 TYR cc_start: 0.8626 (t80) cc_final: 0.8329 (t80)
REVERT: A  388 VAL cc_start: 0.8383 (p) cc_final: 0.8154 (p)
REVERT: A  478 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8387 (tm-30)
REVERT: A  518 TYR cc_start: 0.8038 (t80) cc_final: 0.7473 (t80)
REVERT: A  561 MET cc_start: 0.6928 (tmm) cc_final: 0.6549 (tmm)
REVERT: B  272 MET cc_start: 0.8490 (tmm) cc_final: 0.8227 (tmm)
REVERT: B  275 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8010 (tm-30)
REVERT: B  309 TYR cc_start: 0.7903 (t80) cc_final: 0.7426 (t80)
REVERT: B  466 TYR cc_start: 0.7620 (m-80) cc_final: 0.7355 (m-80)
REVERT: B  503 LEU cc_start: 0.8747 (tp) cc_final: 0.8218 (tt)
REVERT: B  646 CYS cc_start: 0.8022 (m) cc_final: 0.7820 (m)
REVERT: B  697 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6770 (tt0)
REVERT: B  822 TRP cc_start: 0.8658 (t-100) cc_final: 0.8314 (t-100)
  outliers start: 24
  outliers final: 12
  residues processed: 139
  average time/residue: 0.0987
  time to fit residues: 19.0401
Evaluate side-chains
  124 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 111
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  446 GLU
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  566 ASP
Chi-restraints excluded: chain A residue  748 ILE
Chi-restraints excluded: chain B residue  364 ARG
Chi-restraints excluded: chain B residue  409 PHE
Chi-restraints excluded: chain B residue  434 TRP
Chi-restraints excluded: chain B residue  436 THR
Chi-restraints excluded: chain B residue  566 ASP
Chi-restraints excluded: chain B residue  697 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 103 optimal weight:   30.0000
   chunk 13 optimal weight:    0.5980
   chunk 67 optimal weight:   10.0000
   chunk 104 optimal weight:   10.0000
   chunk 82 optimal weight:    0.6980
   chunk 69 optimal weight:    5.9990
   chunk 57 optimal weight:   10.0000
   chunk 60 optimal weight:    0.6980
   chunk 46 optimal weight:    6.9990
   chunk 16 optimal weight:    0.7980
   chunk 105 optimal weight:   10.0000
   overall best weight:    1.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 352 HIS
A 445 GLN
A 498 ASN
** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 659 GLN
B 539 GLN
** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5153 r_free = 0.5153 target = 0.210936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4643 r_free = 0.4643 target = 0.157267 restraints weight = 17483.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.4466 rms_B_bonded: 3.12
r_work: 0.4326 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.4326
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4288
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4288 r_free = 0.4288    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4288 r_free = 0.4288    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.4288
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.2142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9413  Z= 0.160
  Angle     :  0.623   6.359  12807  Z= 0.327
  Chirality :  0.041   0.258   1488
  Planarity :  0.004   0.048   1592
  Dihedral  :  7.287  54.232   1639
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 18.08 %
    Favored  : 79.73 %
  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: -0.05 (0.24), residues: 1142
  helix:  0.93 (0.18), residues: 769
  sheet: -1.97 (0.65), residues: 53
  loop : -2.02 (0.31), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.000   ARG B 723 
 TYR   0.024   0.002   TYR A 465 
 PHE   0.023   0.002   PHE A 418 
 TRP   0.018   0.002   TRP B 434 
 HIS   0.003   0.001   HIS A 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 9413)
  covalent geometry    : angle       0.62325 (12807)
  hydrogen bonds       : bond        0.05249 (  614)
  hydrogen bonds       : angle       4.53807 ( 1818)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 127
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
REVERT: A  386 TYR cc_start: 0.8544 (t80) cc_final: 0.8274 (t80)
REVERT: A  388 VAL cc_start: 0.8535 (p) cc_final: 0.8302 (p)
REVERT: A  413 PHE cc_start: 0.7130 (m-80) cc_final: 0.6921 (m-80)
REVERT: A  452 ARG cc_start: 0.7683 (tmm-80) cc_final: 0.7175 (tmm-80)
REVERT: A  478 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8250 (tm-30)
REVERT: A  518 TYR cc_start: 0.8118 (t80) cc_final: 0.7560 (t80)
REVERT: A  561 MET cc_start: 0.7127 (tmm) cc_final: 0.6819 (tmm)
REVERT: A  758 ASP cc_start: 0.8041 (m-30) cc_final: 0.7636 (t0)
REVERT: B  309 TYR cc_start: 0.7767 (t80) cc_final: 0.7299 (t80)
REVERT: B  466 TYR cc_start: 0.7806 (m-80) cc_final: 0.7586 (m-80)
REVERT: B  503 LEU cc_start: 0.8723 (tp) cc_final: 0.8455 (tp)
REVERT: B  646 CYS cc_start: 0.8028 (m) cc_final: 0.7821 (m)
REVERT: B  697 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6796 (tt0)
REVERT: B  822 TRP cc_start: 0.8635 (t-100) cc_final: 0.8300 (t-100)
  outliers start: 21
  outliers final: 14
  residues processed: 140
  average time/residue: 0.1016
  time to fit residues: 19.4343
Evaluate side-chains
  132 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  397 ASP
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  551 TYR
Chi-restraints excluded: chain A residue  566 ASP
Chi-restraints excluded: chain A residue  748 ILE
Chi-restraints excluded: chain B residue  364 ARG
Chi-restraints excluded: chain B residue  409 PHE
Chi-restraints excluded: chain B residue  434 TRP
Chi-restraints excluded: chain B residue  436 THR
Chi-restraints excluded: chain B residue  505 ILE
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  566 ASP
Chi-restraints excluded: chain B residue  697 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 79 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 88 optimal weight:    6.9990
   chunk 76 optimal weight:    1.9990
   chunk 113 optimal weight:   30.0000
   chunk 105 optimal weight:    6.9990
   chunk 46 optimal weight:    0.2980
   chunk 12 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
A 498 ASN
** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 354 HIS
** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 677 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5186 r_free = 0.5186 target = 0.213952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4688 r_free = 0.4688 target = 0.160356 restraints weight = 17411.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.4492 rms_B_bonded: 3.17
r_work: 0.4350 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.4350
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4267
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4267 r_free = 0.4267    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4267 r_free = 0.4267    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.4267
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.2330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9413  Z= 0.149
  Angle     :  0.623  10.531  12807  Z= 0.320
  Chirality :  0.041   0.161   1488
  Planarity :  0.004   0.049   1592
  Dihedral  :  6.962  53.484   1639
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 19.75 %
    Favored  : 77.64 %
  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:  0.19 (0.24), residues: 1142
  helix:  1.14 (0.18), residues: 766
  sheet: -1.88 (0.64), residues: 53
  loop : -1.98 (0.31), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 723 
 TYR   0.030   0.002   TYR A 465 
 PHE   0.019   0.002   PHE A 418 
 TRP   0.019   0.001   TRP B 360 
 HIS   0.003   0.001   HIS A 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 9413)
  covalent geometry    : angle       0.62278 (12807)
  hydrogen bonds       : bond        0.05070 (  614)
  hydrogen bonds       : angle       4.42465 ( 1818)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 132
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  386 TYR cc_start: 0.8544 (t80) cc_final: 0.8261 (t80)
REVERT: A  388 VAL cc_start: 0.8513 (OUTLIER) cc_final: 0.8276 (p)
REVERT: A  413 PHE cc_start: 0.7058 (m-80) cc_final: 0.6851 (m-80)
REVERT: A  478 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8267 (tm-30)
REVERT: A  483 TYR cc_start: 0.8573 (t80) cc_final: 0.8302 (t80)
REVERT: A  518 TYR cc_start: 0.8095 (t80) cc_final: 0.7566 (t80)
REVERT: A  561 MET cc_start: 0.7153 (tmm) cc_final: 0.6742 (tmm)
REVERT: B  275 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8158 (tm-30)
REVERT: B  309 TYR cc_start: 0.7758 (t80) cc_final: 0.7285 (t80)
REVERT: B  445 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.6883 (tm-30)
REVERT: B  466 TYR cc_start: 0.7718 (m-80) cc_final: 0.7490 (m-80)
REVERT: B  503 LEU cc_start: 0.8720 (tp) cc_final: 0.8444 (tp)
REVERT: B  541 TYR cc_start: 0.7715 (m-10) cc_final: 0.7274 (m-10)
REVERT: B  672 ASP cc_start: 0.8948 (m-30) cc_final: 0.7802 (p0)
REVERT: B  697 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6826 (tt0)
REVERT: B  766 GLN cc_start: 0.9284 (OUTLIER) cc_final: 0.9041 (mp10)
REVERT: B  822 TRP cc_start: 0.8614 (t-100) cc_final: 0.8278 (t-100)
  outliers start: 25
  outliers final: 14
  residues processed: 146
  average time/residue: 0.0932
  time to fit residues: 18.8919
Evaluate side-chains
  140 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 122
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  397 ASP
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  551 TYR
Chi-restraints excluded: chain A residue  566 ASP
Chi-restraints excluded: chain A residue  748 ILE
Chi-restraints excluded: chain B residue  364 ARG
Chi-restraints excluded: chain B residue  409 PHE
Chi-restraints excluded: chain B residue  434 TRP
Chi-restraints excluded: chain B residue  436 THR
Chi-restraints excluded: chain B residue  445 GLN
Chi-restraints excluded: chain B residue  505 ILE
Chi-restraints excluded: chain B residue  566 ASP
Chi-restraints excluded: chain B residue  697 GLU
Chi-restraints excluded: chain B residue  766 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 85 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 38 optimal weight:    6.9990
   chunk 100 optimal weight:    5.9990
   chunk 94 optimal weight:    3.9990
   chunk 110 optimal weight:    0.4980
   chunk 83 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 46 optimal weight:   10.0000
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 665 HIS
** B 557 ASN ** 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 = 0.5175 r_free = 0.5175 target = 0.213149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4682 r_free = 0.4682 target = 0.160169 restraints weight = 17202.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.4507 rms_B_bonded: 3.13
r_work: 0.4369 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.4369
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4294
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4294 r_free = 0.4294    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4294 r_free = 0.4294    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.4294
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7502
moved from start:          0.2528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9413  Z= 0.137
  Angle     :  0.632  14.898  12807  Z= 0.320
  Chirality :  0.041   0.255   1488
  Planarity :  0.004   0.051   1592
  Dihedral  :  6.678  54.054   1639
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 20.69 %
    Favored  : 76.28 %
  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:  0.39 (0.24), residues: 1142
  helix:  1.31 (0.18), residues: 767
  sheet: -1.77 (0.66), residues: 53
  loop : -1.96 (0.31), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 439 
 TYR   0.031   0.001   TYR A 465 
 PHE   0.016   0.001   PHE B 547 
 TRP   0.022   0.001   TRP B 360 
 HIS   0.003   0.001   HIS B 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 9413)
  covalent geometry    : angle       0.63170 (12807)
  hydrogen bonds       : bond        0.04900 (  614)
  hydrogen bonds       : angle       4.30250 ( 1818)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 136
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  388 VAL cc_start: 0.8519 (OUTLIER) cc_final: 0.8291 (p)
REVERT: A  413 PHE cc_start: 0.7011 (m-80) cc_final: 0.6810 (m-80)
REVERT: A  478 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8285 (tm-30)
REVERT: A  518 TYR cc_start: 0.8063 (t80) cc_final: 0.7508 (t80)
REVERT: A  561 MET cc_start: 0.7105 (tmm) cc_final: 0.6800 (tmm)
REVERT: A  758 ASP cc_start: 0.8015 (m-30) cc_final: 0.7643 (t0)
REVERT: B  275 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8284 (tm-30)
REVERT: B  309 TYR cc_start: 0.7706 (t80) cc_final: 0.7239 (t80)
REVERT: B  371 ARG cc_start: 0.8987 (tmm-80) cc_final: 0.8739 (tmm-80)
REVERT: B  372 ILE cc_start: 0.8309 (mm) cc_final: 0.7865 (mm)
REVERT: B  445 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.7019 (tm-30)
REVERT: B  503 LEU cc_start: 0.8679 (tp) cc_final: 0.8408 (tp)
REVERT: B  541 TYR cc_start: 0.7734 (m-10) cc_final: 0.7270 (m-10)
REVERT: B  672 ASP cc_start: 0.8888 (m-30) cc_final: 0.7776 (p0)
REVERT: B  697 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6827 (tt0)
REVERT: B  822 TRP cc_start: 0.8585 (t-100) cc_final: 0.8238 (t-100)
  outliers start: 29
  outliers final: 16
  residues processed: 157
  average time/residue: 0.1046
  time to fit residues: 22.2866
Evaluate side-chains
  147 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  397 ASP
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  551 TYR
Chi-restraints excluded: chain A residue  566 ASP
Chi-restraints excluded: chain A residue  612 THR
Chi-restraints excluded: chain A residue  748 ILE
Chi-restraints excluded: chain B residue  364 ARG
Chi-restraints excluded: chain B residue  409 PHE
Chi-restraints excluded: chain B residue  434 TRP
Chi-restraints excluded: chain B residue  445 GLN
Chi-restraints excluded: chain B residue  505 ILE
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  566 ASP
Chi-restraints excluded: chain B residue  697 GLU
Chi-restraints excluded: chain B residue  766 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 111 optimal weight:   30.0000
   chunk 98 optimal weight:    0.0010
   chunk 95 optimal weight:    0.0980
   chunk 65 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 99 optimal weight:    6.9990
   chunk 23 optimal weight:    0.9990
   chunk 78 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 110 optimal weight:    5.9990
   overall best weight:    0.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 338 GLN
** B 557 ASN ** 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 = 0.5208 r_free = 0.5208 target = 0.216042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4728 r_free = 0.4728 target = 0.163383 restraints weight = 17288.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.4494 rms_B_bonded: 3.21
r_work: 0.4333 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.4333
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4268
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4268 r_free = 0.4268    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4268 r_free = 0.4268    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.4268
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.2742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9413  Z= 0.129
  Angle     :  0.647  16.490  12807  Z= 0.323
  Chirality :  0.040   0.155   1488
  Planarity :  0.004   0.050   1592
  Dihedral  :  6.445  56.317   1639
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 22.99 %
    Favored  : 75.03 %
  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:  0.53 (0.25), residues: 1142
  helix:  1.46 (0.19), residues: 762
  sheet: -1.61 (0.68), residues: 53
  loop : -1.99 (0.31), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 439 
 TYR   0.035   0.001   TYR A 465 
 PHE   0.015   0.001   PHE B 547 
 TRP   0.025   0.001   TRP B 360 
 HIS   0.003   0.001   HIS A 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 9413)
  covalent geometry    : angle       0.64706 (12807)
  hydrogen bonds       : bond        0.04749 (  614)
  hydrogen bonds       : angle       4.18145 ( 1818)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 140
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  309 TYR cc_start: 0.8298 (t80) cc_final: 0.7900 (t80)
REVERT: A  388 VAL cc_start: 0.8420 (OUTLIER) cc_final: 0.8168 (p)
REVERT: A  413 PHE cc_start: 0.7020 (m-80) cc_final: 0.6783 (m-80)
REVERT: A  478 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8348 (tm-30)
REVERT: A  518 TYR cc_start: 0.8010 (t80) cc_final: 0.7466 (t80)
REVERT: A  758 ASP cc_start: 0.7965 (m-30) cc_final: 0.7615 (t0)
REVERT: B  309 TYR cc_start: 0.7665 (t80) cc_final: 0.7231 (t80)
REVERT: B  371 ARG cc_start: 0.9001 (tmm-80) cc_final: 0.8742 (tmm-80)
REVERT: B  372 ILE cc_start: 0.8242 (mm) cc_final: 0.7769 (mm)
REVERT: B  445 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.7124 (tm-30)
REVERT: B  672 ASP cc_start: 0.8920 (m-30) cc_final: 0.7875 (p0)
REVERT: B  697 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6773 (tt0)
REVERT: B  739 ARG cc_start: 0.8251 (ttt180) cc_final: 0.7641 (mtt-85)
REVERT: B  822 TRP cc_start: 0.8579 (t-100) cc_final: 0.8206 (t-100)
  outliers start: 19
  outliers final: 11
  residues processed: 153
  average time/residue: 0.1078
  time to fit residues: 22.5198
Evaluate side-chains
  144 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 130
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  551 TYR
Chi-restraints excluded: chain A residue  566 ASP
Chi-restraints excluded: chain A residue  612 THR
Chi-restraints excluded: chain A residue  748 ILE
Chi-restraints excluded: chain B residue  364 ARG
Chi-restraints excluded: chain B residue  434 TRP
Chi-restraints excluded: chain B residue  445 GLN
Chi-restraints excluded: chain B residue  566 ASP
Chi-restraints excluded: chain B residue  697 GLU
Chi-restraints excluded: chain B residue  766 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 101 optimal weight:    9.9990
   chunk 47 optimal weight:    5.9990
   chunk 73 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   chunk 78 optimal weight:    0.9980
   chunk 19 optimal weight:    6.9990
   chunk 23 optimal weight:    0.8980
   chunk 42 optimal weight:    7.9990
   chunk 61 optimal weight:    0.6980
   chunk 41 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
A 279 ASN
A 498 ASN
B 354 HIS
B 523 GLN
** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5214 r_free = 0.5214 target = 0.216422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4733 r_free = 0.4733 target = 0.163618 restraints weight = 17317.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.4514 rms_B_bonded: 3.24
r_work: 0.4367 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.4367
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4316
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4316 r_free = 0.4316    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4316 r_free = 0.4316    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.4316
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.2870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   9413  Z= 0.141
  Angle     :  0.681  16.692  12807  Z= 0.336
  Chirality :  0.041   0.165   1488
  Planarity :  0.004   0.048   1592
  Dihedral  :  6.396  58.691   1639
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 22.78 %
    Favored  : 74.71 %
  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:  0.59 (0.25), residues: 1142
  helix:  1.49 (0.19), residues: 758
  sheet: -1.55 (0.68), residues: 53
  loop : -1.90 (0.31), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 439 
 TYR   0.040   0.002   TYR A 465 
 PHE   0.016   0.001   PHE A 418 
 TRP   0.026   0.002   TRP B 360 
 HIS   0.005   0.001   HIS B 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 9413)
  covalent geometry    : angle       0.68053 (12807)
  hydrogen bonds       : bond        0.04779 (  614)
  hydrogen bonds       : angle       4.20806 ( 1818)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 131
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  388 VAL cc_start: 0.8462 (OUTLIER) cc_final: 0.8243 (p)
REVERT: A  478 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8356 (tm-30)
REVERT: A  518 TYR cc_start: 0.8024 (t80) cc_final: 0.7470 (t80)
REVERT: A  565 PHE cc_start: 0.5022 (OUTLIER) cc_final: 0.3655 (m-80)
REVERT: B  275 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8121 (tm-30)
REVERT: B  309 TYR cc_start: 0.7700 (t80) cc_final: 0.7245 (t80)
REVERT: B  371 ARG cc_start: 0.8970 (tmm-80) cc_final: 0.8706 (tmm-80)
REVERT: B  372 ILE cc_start: 0.8227 (mm) cc_final: 0.7744 (mm)
REVERT: B  445 GLN cc_start: 0.7434 (OUTLIER) cc_final: 0.7041 (tm-30)
REVERT: B  457 LEU cc_start: 0.8083 (mt) cc_final: 0.7749 (mp)
REVERT: B  672 ASP cc_start: 0.8878 (m-30) cc_final: 0.7854 (p0)
REVERT: B  697 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6350 (tt0)
REVERT: B  701 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8111 (mp10)
REVERT: B  739 ARG cc_start: 0.8237 (ttt180) cc_final: 0.7637 (mtt-85)
REVERT: B  822 TRP cc_start: 0.8555 (t-100) cc_final: 0.8190 (t-100)
  outliers start: 24
  outliers final: 15
  residues processed: 148
  average time/residue: 0.1007
  time to fit residues: 20.4967
Evaluate side-chains
  145 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 125
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  551 TYR
Chi-restraints excluded: chain A residue  565 PHE
Chi-restraints excluded: chain A residue  566 ASP
Chi-restraints excluded: chain A residue  612 THR
Chi-restraints excluded: chain A residue  748 ILE
Chi-restraints excluded: chain B residue  364 ARG
Chi-restraints excluded: chain B residue  409 PHE
Chi-restraints excluded: chain B residue  434 TRP
Chi-restraints excluded: chain B residue  436 THR
Chi-restraints excluded: chain B residue  445 GLN
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  566 ASP
Chi-restraints excluded: chain B residue  697 GLU
Chi-restraints excluded: chain B residue  701 GLN
Chi-restraints excluded: chain B residue  766 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 64 optimal weight:    0.7980
   chunk 57 optimal weight:    6.9990
   chunk 86 optimal weight:    4.9990
   chunk 4 optimal weight:    0.7980
   chunk 104 optimal weight:    4.9990
   chunk 106 optimal weight:    3.9990
   chunk 40 optimal weight:    8.9990
   chunk 78 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 107 optimal weight:    8.9990
   chunk 72 optimal weight:    3.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
A 354 HIS
B 354 HIS
B 443 ASN
B 523 GLN
** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5205 r_free = 0.5205 target = 0.215778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4716 r_free = 0.4716 target = 0.162311 restraints weight = 17329.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.4476 rms_B_bonded: 3.22
r_work: 0.4315 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.4315
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4262
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4262 r_free = 0.4262    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4262 r_free = 0.4262    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.4262
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.2944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   9413  Z= 0.161
  Angle     :  0.724  16.391  12807  Z= 0.352
  Chirality :  0.043   0.323   1488
  Planarity :  0.004   0.047   1592
  Dihedral  :  6.446  59.121   1639
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 23.09 %
    Favored  : 74.19 %
  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:  0.50 (0.25), residues: 1142
  helix:  1.39 (0.19), residues: 765
  sheet: -1.61 (0.68), residues: 53
  loop : -1.91 (0.31), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 439 
 TYR   0.020   0.002   TYR B 541 
 PHE   0.020   0.001   PHE A 418 
 TRP   0.027   0.002   TRP B 360 
 HIS   0.002   0.001   HIS A 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 9413)
  covalent geometry    : angle       0.72389 (12807)
  hydrogen bonds       : bond        0.04858 (  614)
  hydrogen bonds       : angle       4.31622 ( 1818)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 128
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  388 VAL cc_start: 0.8548 (OUTLIER) cc_final: 0.8327 (p)
REVERT: A  478 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8292 (tm-30)
REVERT: A  518 TYR cc_start: 0.8059 (t80) cc_final: 0.7545 (t80)
REVERT: A  565 PHE cc_start: 0.5038 (OUTLIER) cc_final: 0.3853 (m-80)
REVERT: A  758 ASP cc_start: 0.7996 (m-30) cc_final: 0.7661 (t0)
REVERT: B  275 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8060 (tm-30)
REVERT: B  309 TYR cc_start: 0.7710 (t80) cc_final: 0.7233 (t80)
REVERT: B  371 ARG cc_start: 0.8960 (tmm-80) cc_final: 0.8703 (tmm-80)
REVERT: B  372 ILE cc_start: 0.8212 (mm) cc_final: 0.7729 (mm)
REVERT: B  445 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.7122 (tm-30)
REVERT: B  672 ASP cc_start: 0.8884 (m-30) cc_final: 0.7865 (p0)
REVERT: B  697 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6321 (tt0)
REVERT: B  701 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.8017 (mp10)
REVERT: B  822 TRP cc_start: 0.8548 (t-100) cc_final: 0.8174 (t-100)
  outliers start: 26
  outliers final: 16
  residues processed: 146
  average time/residue: 0.0981
  time to fit residues: 19.7617
Evaluate side-chains
  143 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 122
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  397 ASP
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  551 TYR
Chi-restraints excluded: chain A residue  565 PHE
Chi-restraints excluded: chain A residue  566 ASP
Chi-restraints excluded: chain A residue  612 THR
Chi-restraints excluded: chain A residue  748 ILE
Chi-restraints excluded: chain B residue  364 ARG
Chi-restraints excluded: chain B residue  366 THR
Chi-restraints excluded: chain B residue  409 PHE
Chi-restraints excluded: chain B residue  434 TRP
Chi-restraints excluded: chain B residue  436 THR
Chi-restraints excluded: chain B residue  445 GLN
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  566 ASP
Chi-restraints excluded: chain B residue  697 GLU
Chi-restraints excluded: chain B residue  701 GLN
Chi-restraints excluded: chain B residue  766 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 102 optimal weight:    8.9990
   chunk 52 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9990
   chunk 16 optimal weight:    0.4980
   chunk 25 optimal weight:    2.9990
   chunk 38 optimal weight:    8.9990
   chunk 111 optimal weight:   20.0000
   chunk 107 optimal weight:   10.0000
   chunk 72 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
B 354 HIS
B 523 GLN
** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5206 r_free = 0.5206 target = 0.215754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4715 r_free = 0.4715 target = 0.162194 restraints weight = 17421.211|
|-----------------------------------------------------------------------------|
r_work (start): 0.4483 rms_B_bonded: 3.24
r_work: 0.4324 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.4324
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4266
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4266 r_free = 0.4266    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4266 r_free = 0.4266    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.4266
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.3008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9413  Z= 0.153
  Angle     :  0.733  16.955  12807  Z= 0.355
  Chirality :  0.042   0.174   1488
  Planarity :  0.004   0.047   1592
  Dihedral  :  6.414  58.864   1639
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 23.62 %
    Favored  : 74.19 %
  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:  0.53 (0.25), residues: 1142
  helix:  1.42 (0.19), residues: 765
  sheet: -1.52 (0.69), residues: 52
  loop : -1.92 (0.31), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B 723 
 TYR   0.038   0.002   TYR A 465 
 PHE   0.019   0.001   PHE A 418 
 TRP   0.029   0.002   TRP B 360 
 HIS   0.005   0.001   HIS B 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 9413)
  covalent geometry    : angle       0.73285 (12807)
  hydrogen bonds       : bond        0.04822 (  614)
  hydrogen bonds       : angle       4.29512 ( 1818)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 123
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  388 VAL cc_start: 0.8524 (OUTLIER) cc_final: 0.8300 (p)
REVERT: A  439 ARG cc_start: 0.9201 (mmm160) cc_final: 0.8879 (mmm160)
REVERT: A  478 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8277 (tm-30)
REVERT: A  518 TYR cc_start: 0.8072 (t80) cc_final: 0.7514 (t80)
REVERT: A  565 PHE cc_start: 0.5042 (OUTLIER) cc_final: 0.3839 (m-80)
REVERT: A  758 ASP cc_start: 0.7993 (m-30) cc_final: 0.7642 (t0)
REVERT: B  275 GLU cc_start: 0.8376 (tm-30) cc_final: 0.8068 (tm-30)
REVERT: B  309 TYR cc_start: 0.7695 (t80) cc_final: 0.7223 (t80)
REVERT: B  371 ARG cc_start: 0.8962 (tmm-80) cc_final: 0.8704 (tmm-80)
REVERT: B  372 ILE cc_start: 0.8241 (mm) cc_final: 0.7738 (mm)
REVERT: B  445 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.7162 (tm-30)
REVERT: B  672 ASP cc_start: 0.8860 (m-30) cc_final: 0.7857 (p0)
REVERT: B  697 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6333 (tt0)
REVERT: B  701 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7992 (mp10)
REVERT: B  822 TRP cc_start: 0.8549 (t-100) cc_final: 0.8160 (t-100)
  outliers start: 21
  outliers final: 13
  residues processed: 138
  average time/residue: 0.1008
  time to fit residues: 19.2066
Evaluate side-chains
  141 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 123
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  565 PHE
Chi-restraints excluded: chain A residue  566 ASP
Chi-restraints excluded: chain A residue  612 THR
Chi-restraints excluded: chain A residue  748 ILE
Chi-restraints excluded: chain B residue  364 ARG
Chi-restraints excluded: chain B residue  366 THR
Chi-restraints excluded: chain B residue  409 PHE
Chi-restraints excluded: chain B residue  434 TRP
Chi-restraints excluded: chain B residue  445 GLN
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  566 ASP
Chi-restraints excluded: chain B residue  697 GLU
Chi-restraints excluded: chain B residue  701 GLN
Chi-restraints excluded: chain B residue  766 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 15 optimal weight:    3.9990
   chunk 63 optimal weight:    5.9990
   chunk 64 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 93 optimal weight:    8.9990
   chunk 82 optimal weight:    0.6980
   chunk 87 optimal weight:   20.0000
   chunk 12 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
B 354 HIS
** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 783 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5225 r_free = 0.5225 target = 0.217782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4750 r_free = 0.4750 target = 0.164795 restraints weight = 17329.306|
|-----------------------------------------------------------------------------|
r_work (start): 0.4503 rms_B_bonded: 3.24
r_work: 0.4340 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.4340
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4303
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4303 r_free = 0.4303    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4303 r_free = 0.4303    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4303
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.3182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9413  Z= 0.137
  Angle     :  0.719  17.070  12807  Z= 0.347
  Chirality :  0.041   0.164   1488
  Planarity :  0.004   0.047   1592
  Dihedral  :  6.227  59.276   1639
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 23.51 %
    Favored  : 74.19 %
  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:  0.67 (0.25), residues: 1142
  helix:  1.56 (0.19), residues: 762
  sheet: -1.38 (0.71), residues: 52
  loop : -1.95 (0.31), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.000   ARG B 723 
 TYR   0.021   0.001   TYR B 541 
 PHE   0.014   0.001   PHE A 418 
 TRP   0.030   0.002   TRP B 360 
 HIS   0.004   0.001   HIS A 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 9413)
  covalent geometry    : angle       0.71911 (12807)
  hydrogen bonds       : bond        0.04708 (  614)
  hydrogen bonds       : angle       4.20742 ( 1818)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2938.48 seconds
wall clock time: 50 minutes 46.42 seconds (3046.42 seconds total)