Starting phenix.real_space_refine
on Fri Mar 14 01:30:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7dny_30790/03_2025/7dny_30790.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7dny_30790/03_2025/7dny_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7dny_30790/03_2025/7dny_30790.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7dny_30790/03_2025/7dny_30790.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7dny_30790/03_2025/7dny_30790.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7dny_30790/03_2025/7dny_30790.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'TYR:plan': 1, 'GLU: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: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG: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: 6.24, per 1000 atoms: 0.68
  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: 2.38
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.85
  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: 2.55

  Time building geometry restraints manager: 2.78 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 828 or resid 901 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 828 or resid 901 through 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:             2.580
  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:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.400
  Find NCS groups from input model:        0.370
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.790
-------------------------------------------------------------------------------
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= 0.583
  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 : 9.38
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.83 (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
 TRP   0.078   0.005   TRP A 299 
 HIS   0.007   0.001   HIS B 352 
 PHE   0.051   0.004   PHE A 405 
 TYR   0.042   0.004   TYR A 465 
 ARG   0.023   0.001   ARG A 452 

*********************** 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  : 1.030 
Fit side-chains
   revert: symmetry clash
   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: 0.2392
  time to fit residues: 52.2916
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  : 1.225 
-------------------------------------------------------------------------------
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 96 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9990
   chunk 47 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 46 optimal weight:   20.0000
   chunk 89 optimal weight:   30.0000
   chunk 34 optimal weight:   20.0000
   chunk 54 optimal weight:   20.0000
   chunk 66 optimal weight:    0.9990
   chunk 103 optimal weight:    7.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 459 ASN
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5174 r_free = 0.5174 target = 0.212968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4675 r_free = 0.4675 target = 0.159731 restraints weight = 17119.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.4489 rms_B_bonded: 3.09
r_work: 0.4352 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.4352
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4283
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4283 r_free = 0.4283    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 = 0.4281 r_free = 0.4281    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.4281
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.1547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9413  Z= 0.241
  Angle     :  0.682   8.172  12807  Z= 0.361
  Chirality :  0.042   0.150   1488
  Planarity :  0.005   0.071   1592
  Dihedral  :  8.300  59.987   1641
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 12.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 11.49 %
    Favored  : 87.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.24), residues: 1142
  helix:  0.42 (0.18), residues: 777
  sheet: -2.05 (0.67), residues: 53
  loop : -2.29 (0.30), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP B 434 
 HIS   0.009   0.001   HIS A 354 
 PHE   0.027   0.002   PHE A 418 
 TYR   0.023   0.002   TYR A 483 
 ARG   0.008   0.001   ARG A 452 

*********************** 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
  151 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 140
  time to evaluate  : 2.818 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  286 TYR cc_start: 0.7973 (t80) cc_final: 0.6937 (t80)
REVERT: A  386 TYR cc_start: 0.8513 (t80) cc_final: 0.8138 (t80)
REVERT: A  388 VAL cc_start: 0.8514 (p) cc_final: 0.8278 (p)
REVERT: A  478 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8273 (tm-30)
REVERT: A  561 MET cc_start: 0.7108 (tmm) cc_final: 0.6842 (tmm)
REVERT: A  758 ASP cc_start: 0.8082 (m-30) cc_final: 0.7646 (t0)
REVERT: B  272 MET cc_start: 0.8385 (tmm) cc_final: 0.8183 (tmm)
REVERT: B  309 TYR cc_start: 0.7627 (t80) cc_final: 0.7218 (t80)
REVERT: B  370 LEU cc_start: 0.9169 (tp) cc_final: 0.8963 (tp)
REVERT: B  466 TYR cc_start: 0.7729 (m-80) cc_final: 0.7425 (m-80)
REVERT: B  503 LEU cc_start: 0.8738 (tp) cc_final: 0.8460 (tp)
REVERT: B  646 CYS cc_start: 0.8028 (m) cc_final: 0.7818 (m)
REVERT: B  822 TRP cc_start: 0.8642 (t-100) cc_final: 0.8318 (t-100)
  outliers start: 11
  outliers final: 7
  residues processed: 147
  average time/residue: 0.3129
  time to fit residues: 67.4279
Evaluate side-chains
  125 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 118
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
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  446 GLU
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 6 optimal weight:    5.9990
   chunk 71 optimal weight:    1.9990
   chunk 94 optimal weight:    8.9990
   chunk 10 optimal weight:    8.9990
   chunk 82 optimal weight:    0.5980
   chunk 64 optimal weight:    3.9990
   chunk 92 optimal weight:    8.9990
   chunk 79 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9980
   chunk 2 optimal weight:    0.0370
   chunk 21 optimal weight:    3.9990
   overall best weight:    1.3262

-------------------------------------------------------------------------------
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 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 586 GLN
A 659 GLN
** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.5199 r_free = 0.5199 target = 0.215198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4707 r_free = 0.4707 target = 0.161740 restraints weight = 17445.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.4477 rms_B_bonded: 3.20
r_work: 0.4326 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.4326
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4282
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4282 r_free = 0.4282    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4282 r_free = 0.4282    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.4282
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
moved from start:          0.1927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9413  Z= 0.204
  Angle     :  0.616   6.642  12807  Z= 0.324
  Chirality :  0.041   0.209   1488
  Planarity :  0.004   0.058   1592
  Dihedral  :  7.512  58.978   1641
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 15.78 %
    Favored  : 82.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.24), residues: 1142
  helix:  0.93 (0.18), residues: 769
  sheet: -1.97 (0.68), residues: 53
  loop : -2.11 (0.31), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 434 
 HIS   0.014   0.001   HIS A 665 
 PHE   0.023   0.002   PHE A 418 
 TYR   0.034   0.002   TYR A 465 
 ARG   0.005   0.000   ARG A 452 

*********************** 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
  144 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 127
  time to evaluate  : 1.001 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  386 TYR cc_start: 0.8509 (t80) cc_final: 0.8183 (t80)
REVERT: A  388 VAL cc_start: 0.8538 (p) cc_final: 0.8303 (p)
REVERT: A  445 GLN cc_start: 0.7274 (OUTLIER) cc_final: 0.6496 (tm-30)
REVERT: A  478 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8277 (tm-30)
REVERT: A  483 TYR cc_start: 0.8884 (t80) cc_final: 0.8397 (t80)
REVERT: A  561 MET cc_start: 0.7123 (tmm) cc_final: 0.6794 (tmm)
REVERT: B  272 MET cc_start: 0.8389 (tmm) cc_final: 0.8177 (tmm)
REVERT: B  275 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8134 (tm-30)
REVERT: B  309 TYR cc_start: 0.7696 (t80) cc_final: 0.7222 (t80)
REVERT: B  370 LEU cc_start: 0.9178 (tp) cc_final: 0.8968 (tp)
REVERT: B  466 TYR cc_start: 0.7757 (m-80) cc_final: 0.7492 (m-80)
REVERT: B  503 LEU cc_start: 0.8706 (tp) cc_final: 0.8431 (tp)
REVERT: B  656 GLN cc_start: 0.8666 (pp30) cc_final: 0.8081 (mp10)
REVERT: B  697 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6704 (tt0)
REVERT: B  822 TRP cc_start: 0.8635 (t-100) cc_final: 0.8308 (t-100)
  outliers start: 17
  outliers final: 7
  residues processed: 140
  average time/residue: 0.2315
  time to fit residues: 45.0935
Evaluate side-chains
  126 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 117
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  445 GLN
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
Chi-restraints excluded: chain B residue  434 TRP
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 101 optimal weight:    8.9990
   chunk 106 optimal weight:    7.9990
   chunk 38 optimal weight:   10.0000
   chunk 94 optimal weight:    0.3980
   chunk 54 optimal weight:    0.6980
   chunk 91 optimal weight:    0.0870
   chunk 14 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   chunk 62 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 82 optimal weight:    0.8980
   overall best weight:    0.8160

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

Flipped N/Q/H residues before XYZ refinement:
** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 354 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 = 0.5211 r_free = 0.5211 target = 0.216360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4731 r_free = 0.4731 target = 0.163570 restraints weight = 17187.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.4488 rms_B_bonded: 3.22
r_work: 0.4334 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.4334
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4308
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4308 r_free = 0.4308    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4308 r_free = 0.4308    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.4308
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.2211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9413  Z= 0.175
  Angle     :  0.604   9.757  12807  Z= 0.312
  Chirality :  0.040   0.196   1488
  Planarity :  0.004   0.052   1592
  Dihedral  :  6.999  59.962   1641
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 18.60 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.25), residues: 1142
  helix:  1.24 (0.19), residues: 767
  sheet: -1.85 (0.68), residues: 53
  loop : -2.06 (0.31), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 434 
 HIS   0.007   0.001   HIS A 665 
 PHE   0.024   0.001   PHE B 418 
 TYR   0.023   0.001   TYR A 465 
 ARG   0.005   0.000   ARG A 439 

*********************** 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
  145 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 129
  time to evaluate  : 1.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  386 TYR cc_start: 0.8507 (t80) cc_final: 0.8235 (t80)
REVERT: A  388 VAL cc_start: 0.8514 (p) cc_final: 0.8276 (p)
REVERT: A  478 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8335 (tm-30)
REVERT: A  561 MET cc_start: 0.7012 (tmm) cc_final: 0.6736 (tmm)
REVERT: A  758 ASP cc_start: 0.8000 (m-30) cc_final: 0.7624 (t0)
REVERT: B  309 TYR cc_start: 0.7680 (t80) cc_final: 0.7209 (t80)
REVERT: B  370 LEU cc_start: 0.9189 (tp) cc_final: 0.8985 (tp)
REVERT: B  445 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.6855 (tm-30)
REVERT: B  466 TYR cc_start: 0.7752 (m-80) cc_final: 0.7473 (m-80)
REVERT: B  503 LEU cc_start: 0.8710 (tp) cc_final: 0.8453 (tp)
REVERT: B  656 GLN cc_start: 0.8606 (pp30) cc_final: 0.7987 (mp10)
REVERT: B  697 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6823 (tt0)
REVERT: B  822 TRP cc_start: 0.8627 (t-100) cc_final: 0.8297 (t-100)
  outliers start: 16
  outliers final: 10
  residues processed: 141
  average time/residue: 0.2284
  time to fit residues: 44.5771
Evaluate side-chains
  129 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
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  446 GLU
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
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  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 39 optimal weight:    8.9990
   chunk 98 optimal weight:    5.9990
   chunk 99 optimal weight:    7.9990
   chunk 49 optimal weight:    9.9990
   chunk 3 optimal weight:    6.9990
   chunk 111 optimal weight:   30.0000
   chunk 102 optimal weight:    6.9990
   chunk 72 optimal weight:    5.9990
   chunk 79 optimal weight:    5.9990
   chunk 77 optimal weight:    6.9990
   chunk 84 optimal weight:    1.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 316 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 = 0.5165 r_free = 0.5165 target = 0.211186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.4632 r_free = 0.4632 target = 0.155934 restraints weight = 17485.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.4383 rms_B_bonded: 3.06
r_work: 0.4240 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.4240
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4172
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4172 r_free = 0.4172    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4172 r_free = 0.4172    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.4172
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.2258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.063   9413  Z= 0.518
  Angle     :  0.800  10.292  12807  Z= 0.410
  Chirality :  0.048   0.191   1488
  Planarity :  0.004   0.039   1592
  Dihedral  :  7.733  54.208   1641
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 14.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 19.85 %
    Favored  : 77.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.24), residues: 1142
  helix:  0.66 (0.18), residues: 766
  sheet: -2.11 (0.63), residues: 53
  loop : -1.96 (0.31), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 434 
 HIS   0.005   0.001   HIS A 665 
 PHE   0.045   0.003   PHE A 418 
 TYR   0.028   0.003   TYR A 465 
 ARG   0.009   0.001   ARG A 452 

*********************** 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
  148 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 119
  time to evaluate  : 0.969 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  286 TYR cc_start: 0.8018 (t80) cc_final: 0.7462 (t80)
REVERT: A  478 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8271 (tm-30)
REVERT: A  518 TYR cc_start: 0.8196 (t80) cc_final: 0.7628 (t80)
REVERT: A  561 MET cc_start: 0.7175 (tmm) cc_final: 0.6751 (tmm)
REVERT: B  309 TYR cc_start: 0.7953 (t80) cc_final: 0.7490 (t80)
REVERT: B  370 LEU cc_start: 0.9218 (tp) cc_final: 0.8999 (tp)
REVERT: B  372 ILE cc_start: 0.8307 (mm) cc_final: 0.8106 (mm)
REVERT: B  466 TYR cc_start: 0.7784 (m-80) cc_final: 0.7580 (m-80)
REVERT: B  503 LEU cc_start: 0.8776 (tp) cc_final: 0.8195 (tt)
REVERT: B  697 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.6939 (tt0)
REVERT: B  822 TRP cc_start: 0.8611 (t-100) cc_final: 0.8285 (t-100)
  outliers start: 29
  outliers final: 19
  residues processed: 141
  average time/residue: 0.2330
  time to fit residues: 44.9898
Evaluate side-chains
  137 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 117
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  349 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  566 ASP
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  748 ILE
Chi-restraints excluded: chain B residue  271 LEU
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 2 optimal weight:    0.0670
   chunk 42 optimal weight:    9.9990
   chunk 68 optimal weight:    7.9990
   chunk 107 optimal weight:    8.9990
   chunk 101 optimal weight:    6.9990
   chunk 21 optimal weight:    0.5980
   chunk 110 optimal weight:    7.9990
   chunk 109 optimal weight:    6.9990
   chunk 36 optimal weight:    6.9990
   chunk 64 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9980
   overall best weight:    1.8720

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

Flipped N/Q/H residues before XYZ refinement:
** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 498 ASN
** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.5161 r_free = 0.5161 target = 0.211409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4646 r_free = 0.4646 target = 0.157526 restraints weight = 17005.842|
|-----------------------------------------------------------------------------|
r_work (start): 0.4466 rms_B_bonded: 3.09
r_work: 0.4322 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.4322
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4270
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4270 r_free = 0.4270    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 = 0.4270 r_free = 0.4270    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.4270
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.2407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9413  Z= 0.239
  Angle     :  0.671  14.988  12807  Z= 0.339
  Chirality :  0.042   0.269   1488
  Planarity :  0.004   0.045   1592
  Dihedral  :  7.046  52.563   1639
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 20.79 %
    Favored  : 76.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.24), residues: 1142
  helix:  1.07 (0.18), residues: 772
  sheet: -1.87 (0.66), residues: 53
  loop : -1.99 (0.31), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 360 
 HIS   0.004   0.001   HIS A 665 
 PHE   0.020   0.002   PHE A 418 
 TYR   0.031   0.002   TYR A 465 
 ARG   0.007   0.000   ARG A 439 

*********************** 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
  154 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 128
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  388 VAL cc_start: 0.8573 (p) cc_final: 0.8326 (p)
REVERT: A  442 MET cc_start: 0.6599 (tpp) cc_final: 0.6261 (tpt)
REVERT: A  465 TYR cc_start: 0.8853 (m-80) cc_final: 0.8548 (m-80)
REVERT: A  478 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8273 (tm-30)
REVERT: A  518 TYR cc_start: 0.8096 (t80) cc_final: 0.7541 (t80)
REVERT: A  561 MET cc_start: 0.7089 (tmm) cc_final: 0.6757 (tmm)
REVERT: A  758 ASP cc_start: 0.8024 (m-30) cc_final: 0.7666 (t0)
REVERT: B  275 GLU cc_start: 0.8338 (tm-30) cc_final: 0.8005 (tm-30)
REVERT: B  309 TYR cc_start: 0.7786 (t80) cc_final: 0.7286 (t80)
REVERT: B  370 LEU cc_start: 0.9191 (tp) cc_final: 0.8972 (tp)
REVERT: B  503 LEU cc_start: 0.8726 (tp) cc_final: 0.8456 (tp)
REVERT: B  672 ASP cc_start: 0.8932 (m-30) cc_final: 0.7735 (p0)
REVERT: B  675 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7877 (tt)
REVERT: B  676 PHE cc_start: 0.6990 (OUTLIER) cc_final: 0.6744 (m-80)
REVERT: B  697 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6810 (tt0)
REVERT: B  822 TRP cc_start: 0.8588 (t-100) cc_final: 0.8242 (t-100)
  outliers start: 26
  outliers final: 14
  residues processed: 147
  average time/residue: 0.2533
  time to fit residues: 51.9893
Evaluate side-chains
  135 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 1.047 
-------------------------------------------------------------------------------
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  397 ASP
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  384 LEU
Chi-restraints excluded: chain B residue  409 PHE
Chi-restraints excluded: chain B residue  434 TRP
Chi-restraints excluded: chain B residue  566 ASP
Chi-restraints excluded: chain B residue  675 LEU
Chi-restraints excluded: chain B residue  676 PHE
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 3 optimal weight:    0.0770
   chunk 89 optimal weight:   30.0000
   chunk 72 optimal weight:    4.9990
   chunk 52 optimal weight:    6.9990
   chunk 34 optimal weight:   30.0000
   chunk 2 optimal weight:    0.0980
   chunk 80 optimal weight:    1.9990
   chunk 97 optimal weight:    9.9990
   chunk 81 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 9 optimal weight:    5.9990
   overall best weight:    1.0344

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

Flipped N/Q/H residues before XYZ refinement:
** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 586 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 = 0.5204 r_free = 0.5204 target = 0.214870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4710 r_free = 0.4710 target = 0.161981 restraints weight = 17271.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.4480 rms_B_bonded: 3.15
r_work: 0.4329 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.4329
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4278
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4278 r_free = 0.4278    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 = 0.4278 r_free = 0.4278    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.4278
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7507
moved from start:          0.2610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073   9413  Z= 0.198
  Angle     :  0.668  16.197  12807  Z= 0.335
  Chirality :  0.041   0.153   1488
  Planarity :  0.004   0.053   1592
  Dihedral  :  6.679  52.223   1639
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 21.94 %
    Favored  : 75.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.24), residues: 1142
  helix:  1.29 (0.18), residues: 766
  sheet: -1.73 (0.67), residues: 53
  loop : -1.96 (0.31), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 360 
 HIS   0.003   0.001   HIS A 665 
 PHE   0.016   0.001   PHE B 418 
 TYR   0.027   0.002   TYR A 465 
 ARG   0.007   0.000   ARG A 439 

*********************** 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
  156 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 129
  time to evaluate  : 1.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  388 VAL cc_start: 0.8560 (OUTLIER) cc_final: 0.8335 (p)
REVERT: A  445 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.6791 (tm-30)
REVERT: A  478 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8295 (tm-30)
REVERT: A  518 TYR cc_start: 0.8067 (t80) cc_final: 0.7505 (t80)
REVERT: A  561 MET cc_start: 0.7033 (tmm) cc_final: 0.6732 (tmm)
REVERT: B  275 GLU cc_start: 0.8356 (tm-30) cc_final: 0.8049 (tm-30)
REVERT: B  309 TYR cc_start: 0.7715 (t80) cc_final: 0.7293 (t80)
REVERT: B  370 LEU cc_start: 0.9193 (tp) cc_final: 0.8989 (tp)
REVERT: B  541 TYR cc_start: 0.7614 (m-10) cc_final: 0.7407 (m-80)
REVERT: B  672 ASP cc_start: 0.8933 (m-30) cc_final: 0.7784 (p0)
REVERT: B  675 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7899 (tt)
REVERT: B  697 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6797 (tt0)
REVERT: B  822 TRP cc_start: 0.8561 (t-100) cc_final: 0.8205 (t-100)
  outliers start: 27
  outliers final: 14
  residues processed: 150
  average time/residue: 0.3091
  time to fit residues: 64.4727
Evaluate side-chains
  137 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 1.247 
-------------------------------------------------------------------------------
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  445 GLN
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  537 ILE
Chi-restraints excluded: chain B residue  566 ASP
Chi-restraints excluded: chain B residue  675 LEU
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 40 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 43 optimal weight:    5.9990
   chunk 58 optimal weight:    1.9990
   chunk 48 optimal weight:    6.9990
   chunk 99 optimal weight:    4.9990
   chunk 44 optimal weight:    6.9990
   chunk 87 optimal weight:    8.9990
   chunk 101 optimal weight:    8.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 354 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 = 0.5202 r_free = 0.5202 target = 0.214944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4705 r_free = 0.4705 target = 0.161303 restraints weight = 17450.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.4476 rms_B_bonded: 3.21
r_work: 0.4319 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.4319
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4268
|-occupancy refinement: start-------------------------------------------------|
| 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:        6 |
|-----------------------------------------------------------------------------|
|-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:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4268
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.2699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   9413  Z= 0.224
  Angle     :  0.698  15.708  12807  Z= 0.345
  Chirality :  0.042   0.160   1488
  Planarity :  0.004   0.052   1592
  Dihedral  :  6.639  52.907   1639
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 22.68 %
    Favored  : 74.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.24), residues: 1142
  helix:  1.33 (0.18), residues: 766
  sheet: -1.65 (0.69), residues: 53
  loop : -1.95 (0.31), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B 360 
 HIS   0.005   0.001   HIS B 354 
 PHE   0.020   0.001   PHE A 418 
 TYR   0.034   0.002   TYR A 465 
 ARG   0.007   0.000   ARG A 439 

*********************** 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
  149 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 125
  time to evaluate  : 1.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  388 VAL cc_start: 0.8531 (OUTLIER) cc_final: 0.8309 (p)
REVERT: A  478 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8320 (tm-30)
REVERT: A  518 TYR cc_start: 0.8014 (t80) cc_final: 0.7453 (t80)
REVERT: A  561 MET cc_start: 0.6986 (tmm) cc_final: 0.6786 (tmm)
REVERT: A  565 PHE cc_start: 0.5123 (OUTLIER) cc_final: 0.3704 (m-80)
REVERT: A  758 ASP cc_start: 0.7989 (m-30) cc_final: 0.7662 (t0)
REVERT: B  309 TYR cc_start: 0.7786 (t80) cc_final: 0.7370 (t80)
REVERT: B  371 ARG cc_start: 0.9026 (tmm-80) cc_final: 0.8698 (ttp80)
REVERT: B  672 ASP cc_start: 0.8921 (m-30) cc_final: 0.7799 (p0)
REVERT: B  697 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6762 (tt0)
REVERT: B  822 TRP cc_start: 0.8554 (t-100) cc_final: 0.8198 (t-100)
  outliers start: 24
  outliers final: 14
  residues processed: 145
  average time/residue: 0.3367
  time to fit residues: 67.3244
Evaluate side-chains
  137 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 2.634 
-------------------------------------------------------------------------------
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  409 PHE
Chi-restraints excluded: chain B residue  434 TRP
Chi-restraints excluded: chain B residue  537 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 39 optimal weight:    7.9990
   chunk 69 optimal weight:   10.0000
   chunk 8 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   chunk 113 optimal weight:   40.0000
   chunk 24 optimal weight:    0.7980
   chunk 14 optimal weight:    0.8980
   chunk 94 optimal weight:    7.9990
   chunk 33 optimal weight:    8.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 498 ASN
A 586 GLN
B 354 HIS
** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5234 r_free = 0.5234 target = 0.223866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4664 r_free = 0.4664 target = 0.156615 restraints weight = 17350.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.4454 rms_B_bonded: 3.62
r_work: 0.4303 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.4303
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4246
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4246 r_free = 0.4246    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4246 r_free = 0.4246    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.4246
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.2797

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= 0.227
  Angle     :  0.710  15.590  12807  Z= 0.349
  Chirality :  0.043   0.318   1488
  Planarity :  0.004   0.052   1592
  Dihedral  :  6.595  53.675   1639
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 23.09 %
    Favored  : 74.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.25), residues: 1142
  helix:  1.32 (0.18), residues: 766
  sheet: -1.60 (0.71), residues: 53
  loop : -1.95 (0.31), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP B 360 
 HIS   0.005   0.001   HIS B 354 
 PHE   0.019   0.001   PHE A 418 
 TYR   0.037   0.002   TYR A 465 
 ARG   0.007   0.000   ARG A 439 

*********************** 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
  149 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 125
  time to evaluate  : 1.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  388 VAL cc_start: 0.8522 (OUTLIER) cc_final: 0.8304 (p)
REVERT: A  413 PHE cc_start: 0.7213 (m-80) cc_final: 0.6866 (m-80)
REVERT: A  445 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.6644 (tm-30)
REVERT: A  452 ARG cc_start: 0.7509 (tmm-80) cc_final: 0.7060 (tmm-80)
REVERT: A  478 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8342 (tm-30)
REVERT: A  518 TYR cc_start: 0.8025 (t80) cc_final: 0.7460 (t80)
REVERT: A  561 MET cc_start: 0.6925 (tmm) cc_final: 0.6626 (tmm)
REVERT: A  758 ASP cc_start: 0.7966 (m-30) cc_final: 0.7636 (t0)
REVERT: B  275 GLU cc_start: 0.8415 (tm-30) cc_final: 0.7809 (tm-30)
REVERT: B  309 TYR cc_start: 0.7795 (t80) cc_final: 0.7345 (t80)
REVERT: B  371 ARG cc_start: 0.9025 (tmm-80) cc_final: 0.8679 (ttp80)
REVERT: B  457 LEU cc_start: 0.8186 (mt) cc_final: 0.7902 (mp)
REVERT: B  672 ASP cc_start: 0.8894 (m-30) cc_final: 0.7798 (p0)
REVERT: B  697 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6821 (tt0)
REVERT: B  822 TRP cc_start: 0.8550 (t-100) cc_final: 0.8170 (t-100)
  outliers start: 24
  outliers final: 17
  residues processed: 143
  average time/residue: 0.3025
  time to fit residues: 59.1930
Evaluate side-chains
  140 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 120
  time to evaluate  : 1.173 
-------------------------------------------------------------------------------
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  445 GLN
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  333 LEU
Chi-restraints excluded: chain B residue  364 ARG
Chi-restraints excluded: chain B residue  386 TYR
Chi-restraints excluded: chain B residue  409 PHE
Chi-restraints excluded: chain B residue  434 TRP
Chi-restraints excluded: chain B residue  537 ILE
Chi-restraints excluded: chain B residue  566 ASP
Chi-restraints excluded: chain B residue  697 GLU
Chi-restraints excluded: chain B residue  748 ILE
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 112 optimal weight:   20.0000
   chunk 94 optimal weight:    8.9990
   chunk 9 optimal weight:    1.9990
   chunk 86 optimal weight:    0.6980
   chunk 107 optimal weight:    8.9990
   chunk 7 optimal weight:    1.9990
   chunk 90 optimal weight:   10.0000
   chunk 12 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9980
   chunk 49 optimal weight:   10.0000
   chunk 101 optimal weight:    5.9990
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 498 ASN
A 586 GLN
B 354 HIS
** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 783 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5196 r_free = 0.5196 target = 0.214199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4694 r_free = 0.4694 target = 0.160562 restraints weight = 17497.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.4461 rms_B_bonded: 3.10
r_work: 0.4312 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.4312
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4235
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4235 r_free = 0.4235    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4235 r_free = 0.4235    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4235
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.2835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   9413  Z= 0.282
  Angle     :  0.751  15.123  12807  Z= 0.368
  Chirality :  0.044   0.182   1488
  Planarity :  0.004   0.050   1592
  Dihedral  :  6.682  52.469   1639
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 12.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 23.41 %
    Favored  : 73.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.24), residues: 1142
  helix:  1.22 (0.18), residues: 769
  sheet: -1.64 (0.71), residues: 53
  loop : -1.88 (0.32), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 360 
 HIS   0.003   0.001   HIS B 354 
 PHE   0.024   0.002   PHE A 418 
 TYR   0.022   0.002   TYR A 550 
 ARG   0.008   0.000   ARG A 439 

********************** 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
  151 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 124
  time to evaluate  : 0.952 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  388 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8343 (p)
REVERT: A  445 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.6696 (tm-30)
REVERT: A  452 ARG cc_start: 0.7512 (tmm-80) cc_final: 0.7110 (tmm-80)
REVERT: A  478 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8287 (tm-30)
REVERT: A  518 TYR cc_start: 0.8083 (t80) cc_final: 0.7570 (t80)
REVERT: A  561 MET cc_start: 0.7118 (tmm) cc_final: 0.6858 (tmm)
REVERT: A  565 PHE cc_start: 0.5234 (OUTLIER) cc_final: 0.3758 (m-80)
REVERT: B  309 TYR cc_start: 0.7778 (t80) cc_final: 0.7329 (t80)
REVERT: B  371 ARG cc_start: 0.8975 (tmm-80) cc_final: 0.8644 (ttp80)
REVERT: B  672 ASP cc_start: 0.8870 (m-30) cc_final: 0.7749 (p0)
REVERT: B  697 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6815 (tt0)
REVERT: B  822 TRP cc_start: 0.8544 (t-100) cc_final: 0.8158 (t-100)
  outliers start: 27
  outliers final: 20
  residues processed: 142
  average time/residue: 0.2343
  time to fit residues: 45.1471
Evaluate side-chains
  143 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 119
  time to evaluate  : 1.073 
-------------------------------------------------------------------------------
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  445 GLN
Chi-restraints excluded: chain A residue  446 GLU
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  333 LEU
Chi-restraints excluded: chain B residue  364 ARG
Chi-restraints excluded: chain B residue  386 TYR
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  527 VAL
Chi-restraints excluded: chain B residue  537 ILE
Chi-restraints excluded: chain B residue  566 ASP
Chi-restraints excluded: chain B residue  697 GLU
Chi-restraints excluded: chain B residue  748 ILE
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 72 optimal weight:    4.9990
   chunk 111 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 101 optimal weight:    7.9990
   chunk 92 optimal weight:   20.0000
   chunk 38 optimal weight:    1.9990
   chunk 37 optimal weight:    7.9990
   chunk 47 optimal weight:    5.9990
   chunk 81 optimal weight:    2.9990
   chunk 10 optimal weight:    6.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 586 GLN
B 354 HIS
** B 443 ASN ** 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 = 0.5186 r_free = 0.5186 target = 0.212679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4672 r_free = 0.4672 target = 0.158219 restraints weight = 17150.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.4415 rms_B_bonded: 3.14
r_work: 0.4255 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.4255
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4238
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4238 r_free = 0.4238    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4238 r_free = 0.4238    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4238
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.2843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071   9413  Z= 0.329
  Angle     :  0.783  14.507  12807  Z= 0.382
  Chirality :  0.045   0.204   1488
  Planarity :  0.004   0.050   1592
  Dihedral  :  6.947  50.328   1639
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 13.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 23.82 %
    Favored  : 73.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.24), residues: 1142
  helix:  1.06 (0.18), residues: 769
  sheet: -1.62 (0.70), residues: 52
  loop : -1.87 (0.32), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 360 
 HIS   0.003   0.001   HIS B 354 
 PHE   0.029   0.002   PHE A 418 
 TYR   0.043   0.002   TYR A 465 
 ARG   0.008   0.000   ARG A 439 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6076.80 seconds
wall clock time: 107 minutes 35.45 seconds (6455.45 seconds total)